NeurodataWithoutBorders
Programmatically find all the time series in any NWB file
Hello everyone. I've been using your API to develop my GSoC project and one of my tasks was to find a way to programmatically find all the time series present in any NWB 2.x file. I've tried to develop this as follows:
def _get_data_interfaces(self, node):
"""Given a NWBHDF5IO returns all the data_interfaces objects presents on it."""
data_interfaces_list = []
for child in node.children:
if isinstance(child, NWBDataInterface):
data_interfaces_list.append(child)
data_interfaces_list += self._get_data_interfaces(child)
return data_interfaces_list
def _get_timeseries(self):
"""Given all the nwb_data_interfaces returns all of those that are timeseries objects."""
time_series_list = []
for data_interface in self.nwb_data_interfaces_list:
if isinstance(data_interface, TimeSeries):
time_series_list.append(data_interface)
return time_series_list
I believe this returns all the TimeSeries objects, then I simply run over each one of them to get mono dimensional time series easily plottable:
def get_mono_dimensional_timeseries(self, values):
"""Given a timeseries object returns all mono dimensional timeseries presents on it."""
mono_time_series_list = []
if isinstance(values, collections.Iterable):
try:
data = [float(i) for i in values]
mono_time_series_list.append(data)
except:
for inner_list in values:
mono_time_series_list += self.get_mono_dimensional_timeseries(inner_list)
return mono_time_series_list
I would like to get your opinion on this. I wasn't able to find this feature in your API. Do you think it has any value? Would you do this any other way? I understand that this is not a typical issue, so apologies in advance if it should be asked elsewhere. :pray:
Hi @afonsobspinto, thanks for working on this. I know @ajtritt has been working on query functionality that looks a lot like this, but it's not finished/supported/documented. He may be able to point you in the direction of these tools so you can use them for your own work. In the meantime, keep hacking away!
hey @afonsobspinto, look at the getitem implementation on LabelledDict. I apologize for the lack of documentation--as @bendichter said, it's not finished.
https://github.com/NeurodataWithoutBorders/pynwb/blob/6d2cc9f8ed3ab1a67e2da2fb4fec77029aed2215/src/pynwb/core.py#L43
@afonsobspinto. Maybe The NWB query engine: https://github.com/jezekp/NwbQueryEngine could be useful too
