Multiple subquery examplesΒΆ
Queries can be created by combining multiple subqueries. Some examples along with the output are shown in this section. The datasets (nwb files) used in the examples are:
- The first 16 files in the alm-1 data set at CRCNS.org (http://crcns.org/data-sets/motor-cortex/alm-1), which contains anterior motor cortex recordings from the Svoboda Lab at Janelia Farm. The total size of these data files is (2.2 GB).
- NWB-formatted dataset from Steinmetz et al. Nature 2019. Available at: https://figshare.com/articles/Datasets_from_Steinmetz_et_al_2019_in_NWB_format/11274968 File: Steinmetz2019_Forssmann_2017-11-05.nwb (267.96 MB)
In the sample queries (done with the query_index.py utility) the index file (nwb_index.db) is located in the ../../sample_data` directory). The output would be the same if the search_nwb.py utility is used if a directory containing the nwb files was specified as the <path> in the search_nwb command as described in section search_nwb.py usage. The format of the output is as described in section Format of query output.
Query:
$ python -m nwbindexer.query_index ../../sample_data '/general/subject: (age LIKE "%3 months 16 days%" & species LIKE "%Mus musculu%") & /:file_create_date LIKE "%2017-04%" & /epochs/* : start_time < 15'
Output is:
Using index_path: '../../sample_data/nwb_index.db'
Opening '../../sample_data/nwb_index.db'
Found 2 matching files:
[ { 'file': './nwb1/data_structure_ANM210862_20130627.nwb',
'subqueries': [ [ { 'node': '/general/subject',
'vind': { 'age': '3 months 16 days weeks',
'species': 'Mus musculus'},
'vtbl': {}}],
[ { 'node': '/',
'vind': { 'file_create_date': '2017-04-24T11:32:54.215883'},
'vtbl': {}}],
[ { 'node': '/epochs/trial_001',
'vind': {'start_time': 2.284463},
'vtbl': {}}]]},
{ 'file': './nwb1/data_structure_ANM210863_20130627.nwb',
'subqueries': [ [ { 'node': '/general/subject',
'vind': { 'age': '3 months 16 days weeks',
'species': 'Mus musculus'},
'vtbl': {}}],
[ { 'node': '/',
'vind': { 'file_create_date': '2017-04-24T11:32:54.076284'},
'vtbl': {}}],
[ { 'node': '/epochs/trial_001',
'vind': {'start_time': 2.222392},
'vtbl': {}}]]}]
Query:
python -m nwbindexer.query_index ../../sample_data 'intervals/trials: id, visual_stimulus_time, visual_stimulus_left_contrast == 0.25 & visual_stimulus_right_contrast == 0.25'
Output:
Using index_path: '../../sample_data/nwb_index.db'
Opening '../../sample_data/nwb_index.db'
Found 1 matching files:
[ { 'file': './steinmentz2019/Steinmetz2019_Forssmann_2017-11-05.nwb',
'subqueries': [ [ { 'node': '/intervals/trials',
'vind': {},
'vtbl': { 'child_names': [ 'id',
'visual_stimulus_time',
'visual_stimulus_left_contrast',
'visual_stimulus_right_contrast'],
'combined': [ { 'id': 95,
'visual_stimulus_left_contrast': 0.25,
'visual_stimulus_right_contrast': 0.25,
'visual_stimulus_time': 468.198},
{ 'id': 150,
'visual_stimulus_left_contrast': 0.25,
'visual_stimulus_right_contrast': 0.25,
'visual_stimulus_time': 697.717}],
'row_values': [ ( 95,
468.198,
0.25,
0.25),
( 150,
697.717,
0.25,
0.25)]}}]]}]