def fetch_particle_space(self, **kwargs):
"""Property getter for particle_space
"""
# examine cache
uri = self.parent.request_data(UriSpec, **kwargs)
if 'index' in kwargs:
index = kwargs['index']
else:
index = 0
if not (self._uri == uri and self._index == index):
self._particle_space = None
self._uri = uri
if self._particle_space:
pass
else: # self._particle_space is None
if uri is None:
return
debug('spatiocyte data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc + parsed.path
self._particle_space = self.load_spatiocyte_file(fullpath, index)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
def selected_data(self):
if self.index_cursor in range(-self.n_data, self.n_data):
debug("retriving data at index=%s" %self.index_cursor)
return self.parent.request_data(Hdf5DataSpec, index=self.index_cursor)
else:
warning('Index cursor is set to wrong value.')
return None
def fetch_particle_space(self, **kwargs):
"""Property getter for particle_space
"""
# examine cache
uri = self.parent.request_data(UriSpec, **kwargs)
if 'index' in kwargs:
index = kwargs['index']
else:
index = 0
if not (self._uri == uri and self._index == index):
self._particle_space = None
self._uri = uri
if self._particle_space:
pass
else: # self._particle_space is None
if uri is None:
return
debug('spatiocyte data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc + parsed.path
self._particle_space = self.load_spatiocyte_file(
fullpath, index)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
def selected_data(self):
if self.index_cursor in range(-self.n_data, self.n_data):
debug("retriving data at index=%s" % self.index_cursor)
return self.parent.request_data(Hdf5DataSpec,
index=self.index_cursor)
else:
warning('Index cursor is set to wrong value.')
return None
def time_course(self):
"""Returns dictionary of species_name->number-of-particles.
"""
n_items = self.parent.request_data(NumberOfItemsSpec)
populations = {}
for i in range(n_items):
chunk = self.parent.request_data(Hdf5DataSpec, index=i)
if chunk == None:
warning("No data available for index=%d." % (i))
data_section = chunk.get("/data")
if data_section == None or len(data_section.values()) < 1:
warning("Invalid Data section for index=%d." % (i))
continue
data = data_section.values()[0]
ts = data.attrs.get("t")
particles = data.get("particles")
if ts == None or particles == None:
warning("Invalid timestamp/particles")
species_section = chunk.get("/species")
if species_section == None:
warning("No species table for index=%d" % (i))
continue
# iterate for species...
for id, name, radius, dvalue in species_section:
# count number of particles
n_particles = sum(particles["species_id"] == id)
bin_ = populations.setdefault(name, [])
bin_.append((ts, n_particles))
print populations
return populations
def time_course(self):
"""Returns dictionary of species_name->number-of-particles.
"""
n_items = self.parent.request_data(NumberOfItemsSpec)
populations = {}
for i in range(n_items):
chunk = self.parent.request_data(Hdf5DataSpec, index=i)
if chunk == None:
warning('No data available for index=%d.' % (i))
data_section = chunk.get('/data')
if data_section == None or len(data_section.values()) < 1:
warning('Invalid Data section for index=%d.' % (i))
continue
data = data_section.values()[0]
ts = data.attrs.get('t')
particles = data.get('particles')
if ts == None or particles == None:
warning('Invalid timestamp/particles')
species_section = chunk.get('/species')
if species_section == None:
warning('No species table for index=%d' % (i))
continue
# iterate for species...
for id, name, radius, dvalue in species_section:
# count number of particles
n_particles = sum(particles['species_id'] == id)
bin_ = populations.setdefault(name, [])
bin_.append((ts, n_particles))
print populations
return populations
def hdf5_data(self):
"""Property getter for hdf5_data
"""
# examine cache
uri = self.parent.request_data(UriSpec)
if not (self._uri == uri):
self._hdf5_data = None
self._uri = uri
if self._hdf5_data:
pass
else: # self._hdf5_data is None
if uri is None:
return
debug('hdf5 data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc + parsed.path
if os.path.exists(fullpath):
self._hdf5_data = File(fullpath)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
def hdf5_data(self):
"""Property getter for hdf5_data
"""
# examine cache
uri = self.parent.request_data(UriSpec)
if not (self._uri==uri):
self._hdf5_data = None
self._uri = uri
if self._hdf5_data:
pass
else: # self._hdf5_data is None
if uri is None:
return
debug('hdf5 data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc+parsed.path
if os.path.exists(fullpath):
self._hdf5_data = File(fullpath)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
