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change repro add skeleton for stimulus class

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Jan Grewe 2019-03-11 19:49:54 +01:00
parent c6fc8a857a
commit 8fb7d476e8
2 changed files with 22 additions and 6 deletions
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25
database.py
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@ -165,7 +165,7 @@ class CellDatasetMap(dj.Manual):
@schema @schema
class RePro(dj.Manual): class Repro(dj.Manual):
definition = """ definition = """
repro_id : varchar(512) repro_id : varchar(512)
run : smallint run : smallint
@ -173,17 +173,30 @@ class RePro(dj.Manual):
---- ----
repro_name : varchar(512) repro_name : varchar(512)
settings : varchar(3000) settings : varchar(3000)
start : float
duration : float
""" """
@staticmethod @staticmethod
def get_template_tuple(repro_id=None): def get_template_tuple(repro_id=None):
tup = dict(repro_id=None, dataset_id=None, run=0, repro_name="", settings=None) tup = dict(repro_id=None, dataset_id=None, run=0, repro_name="", settings=None, start=None, duration=None)
if repro_id is not None: if repro_id is not None:
d = dict((RePro() & {"repro_id": repro_id}).fetch1()) d = dict((RePro() & {"repro_id": repro_id}).fetch1())
return d return d
return tup return tup
@schema
class Stimulus(dj.Manual):
definition = """
stimulus_id : int
-> Repro
---
settings : varchar(3000)
start : float
duration : float
"""
def populate_datasets(data_path): def populate_datasets(data_path):
print("Importing dataset %s" % data_path) print("Importing dataset %s" % data_path)
if not os.path.exists(data_path): if not os.path.exists(data_path):
@ -315,7 +328,7 @@ def populate_repros(data_path):
if len(rs) == 0: if len(rs) == 0:
continue continue
rs = rs[0] rs = rs[0]
rp = RePro.get_template_tuple() rp = Repro.get_template_tuple()
rp["run"] = rs["Run"] rp["run"] = rs["Run"]
rp["repro_name"] = rs["RePro"] rp["repro_name"] = rs["RePro"]
rp["dataset_id"] = dataset["dataset_id"] rp["dataset_id"] = dataset["dataset_id"]
@ -325,7 +338,9 @@ def populate_repros(data_path):
rp["settings"] = ut.nix_metadata_to_yaml(settings[0]) rp["settings"] = ut.nix_metadata_to_yaml(settings[0])
else: else:
rp["settings"] = ut.nix_metadata_to_yaml(t.metadata) rp["settings"] = ut.nix_metadata_to_yaml(t.metadata)
RePro.insert1(rp, skip_duplicates=True) rp["start"] = t.position[0]
rp["duration"] = t.extent[0]
Repro.insert1(rp, skip_duplicates=True)
f.close() f.close()
f = None f = None
else: else:
@ -353,6 +368,6 @@ def populate(datasets):
if __name__ == "__main__": if __name__ == "__main__":
# data_dir = "../../science/high_frequency_chirps/data" # data_dir = "../../science/high_frequency_chirps/data"
data_dir = "../high_freq_chirps/data" data_dir = "../high_freq_chirps/data"
datasets = glob.glob(os.path.join(data_dir, '2018*')) datasets = glob.glob(os.path.join(data_dir, '2018-11-20*'))
# drop_tables() # drop_tables()
populate(datasets) populate(datasets)

3
util.py
View File

@ -103,12 +103,13 @@ def nix_metadata_to_yaml(section, cur_depth=0, val_count=1):
if __name__ == "__main__": if __name__ == "__main__":
nix_file = "../../science/high_frequency_chirps/data/2018-11-09-aa-invivo-1/2018-11-09-aa-invivo-1.nix" nix_file = "../../science/high_freq_chirps/data/2018-11-09-aa-invivo-1/2018-11-09-aa-invivo-1.nix"
f = nix.File.open(nix_file, nix.FileMode.ReadOnly) f = nix.File.open(nix_file, nix.FileMode.ReadOnly)
b = f.blocks[0] b = f.blocks[0]
yml = nix_metadata_to_yaml(b.tags[0].metadata) yml = nix_metadata_to_yaml(b.tags[0].metadata)
print(yml) print(yml)
print("-"* 80) print("-"* 80)
print(nix_metadata_to_yaml(b.metadata)) print(nix_metadata_to_yaml(b.metadata))
embed()
f.close() f.close()