def run(self):
while True:
overwrite = self.get_parameter("overwrite")
packet = self.receive("in")
try:
log.debug("%s received %s",
self.__class__.__name__,
packet)
file_name = packet.get("file_name")
log.debug("with path %s", file_name)
output_file = h5py.File(file_name)
output_group_name = self.get_parameter("group")
output_group = output_file.require_group(output_group_name)
for key in packet.get_attribute_names():
value = packet.get(key)
log.debug("%s: read attribute %s=%s",
self.__class__.__name__,
key, value)
if not isinstance(value, np.ndarray):
log.debug("%s is not a ndarray, skipping",
type(value))
continue
if key in output_group and overwrite:
del output_group[key]
elif key in output_group and not overwrite:
log.debug("dataset exists, not overwriting")
continue
output_group[key] = value
log.debug("""
%s: written dataset %s
with shape %s
to file %s group %s
""",
self.__class__.__name__,
key,
value.shape,
file_name,
output_group_name)
output_file.close()
except:
log.error('Component Failed: %s',
self.__class__.__name__, exc_info=True)
# yield the CPU, allowing another component to run
self.yield_ctrl()
def run(self):
# Define our components entry point
while True:
# for each file name string waiting on our input port
for packet in self.receive_all("in"):
if packet is not None:
input_file = False
try:
log.debug("%s received %s",
self.__class__.__name__,
packet)
log.debug("with file name %s and data %s",
packet.get("file_name"),
packet.get("data"))
file_name = packet.get("file_name")
object_name = packet.get("data")
input_file = h5py.File(file_name)
input_object = [
dataset[...]
for dataset in input_file[object_name].values()
if isinstance(dataset, h5py.Dataset)]
attrs = [
dataset.attrs
for dataset in input_file[object_name].values()
if isinstance(dataset, h5py.Dataset)][0]
#add info from first dataset
for key, value in attrs.items():
packet.set(key, value)
log.debug("%s found %d datasets",
self.__class__.__name__,
len(input_object))
packet.set("data", input_object)
except:
log.error('%s failed while reading %s',
self.__class__.__name__,
file_name, exc_info=True)
finally:
if input_file:
input_file.close()
# send the packet to the next component
self.send('out', packet)
# yield the CPU, allowing another component to run
self.yield_ctrl()
def run(self):
# Define our components entry point
while True:
# for each file name string waiting on our input port
for packet in self.receive_all("in"):
log.debug("%s received %s %s",
self.__class__.__name__,
packet.get("file_name"),
packet.get("data"))
try:
file_name = packet.get("file_name")
object_name = packet.get("data")
input_file = h5py.File(file_name)
input_object = input_file[object_name]
self.files.append(input_file)
packet.set("data", input_object)
except:
log.error('%s failed while reading %s',
self.__class__.__name__,
file_name, exc_info=True)
# send the packet to the next component
self.send('out', packet)
# yield the CPU, allowing another component to run
self.yield_ctrl()
