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baseline data should now work with frontend classes

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This commit is contained in:
Jan Grewe 2019-09-18 18:14:06 +02:00
parent c4bc3e064a
commit d918373564
1 changed files with 22 additions and 22 deletions
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44
fishbook/baseline_data.py
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@ -1,14 +1,17 @@
__package__ = "fishbook" from fishbook.fishbook import Dataset, RePro
from fishbook.fishbook import Dataset import numpy as np
import nixio as nix
import os
from IPython import embed from IPython import embed
class BaselineData(object): class BaselineData(object):
def __init__(self, dataset:Dataset): def __init__(self, dataset:Dataset):
self.__data = [] self.__data = []
self.__dataset = dataset self.__dataset = dataset
self.__cell = dataset.cells[0] self.__cell = dataset.cells[0] # Beware: Assumption that there is only a single cell
self._get_data() self._get_data()
def _get_data(self): def _get_data(self):
@ -16,12 +19,12 @@ class BaselineData(object):
self.__data = [] self.__data = []
self.__data = [] self.__data = []
repros = (Repros & self.__dataset & "repro_name like 'BaselineActivity%'") repros = RePro.find_repros("BaselineActivity", cell_id=self.__cell.cell_id)
for r in repros: for r in repros:
self.__data.append(self.__read_data(r)) self.__data.append(self.__read_data(r))
def __read_data(self, r:Repros): def __read_data(self, r:RePro):
if self.__dataset["has_nix"]: if self.__dataset.has_nix:
return self.__read_data_from_nix(r) return self.__read_data_from_nix(r)
else: else:
return self.__read_data_from_directory(r) return self.__read_data_from_directory(r)
@ -30,7 +33,6 @@ class BaselineData(object):
def dataset(self): def dataset(self):
return self.__dataset return self.__dataset
@property
def data(self, index:int=0): def data(self, index:int=0):
return self.__data[0] if len(self.__data) >= index else None return self.__data[0] if len(self.__data) >= index else None
@ -39,16 +41,16 @@ class BaselineData(object):
return len(self.__data) return len(self.__data)
def __str__(self): def __str__(self):
str = "Baseline data of %s " % self.__dataset str = "Baseline data of cell %s " % self.__cell.cell_id
def __read_data_from_nix(self, r)->np.ndarray: def __read_data_from_nix(self, r:RePro)->np.ndarray:
data_source = os.path.join(self.__dataset["data_source"], self.__dataset["dataset_id"] + ".nix") data_source = os.path.join(self.__dataset.data_source, self.__dataset.dataset_id + ".nix")
if not os.path.exists(data_source): if not os.path.exists(data_source):
print("Data not found! Trying from folder") print("Data not found! Trying from directory")
return self.__read_data_from_directory(r) return self.__read_data_from_directory(r)
f = nix.File.open(data_source, nix.FileMode.ReadOnly) f = nix.File.open(data_source, nix.FileMode.ReadOnly)
b = f.blocks[0] b = f.blocks[0]
t = b.tags[r["repro_id"]] t = b.tags[r.repro_id]
if not t: if not t:
print("Tag not found!") print("Tag not found!")
data = t.retrieve_data("Spikes-1")[:] data = t.retrieve_data("Spikes-1")[:]
@ -57,7 +59,7 @@ class BaselineData(object):
def __read_data_from_directory(self, r)->np.ndarray: def __read_data_from_directory(self, r)->np.ndarray:
data = [] data = []
data_source = os.path.join(self.__dataset["data_source"], "basespikes1.dat") data_source = os.path.join(self.__dataset.data_source, "basespikes1.dat")
if os.path.exists(data_source): if os.path.exists(data_source):
found_run = False found_run = False
with open(data_source, 'r') as f: with open(data_source, 'r') as f:
@ -65,11 +67,12 @@ class BaselineData(object):
while l: while l:
if "index" in l: if "index" in l:
index = int(l.strip("#").strip().split(":")[-1]) index = int(l.strip("#").strip().split(":")[-1])
found_run = index == r["run"] found_run = index == r.run
if l.startswith("#Key") and found_run: if l.startswith("#Key") and found_run:
data = self.__do_read(f) data = self.__do_read(f)
break break
l = f.readline() l = f.readline()
embed()
return data return data
def __do_read(self, f)->np.ndarray: def __do_read(self, f)->np.ndarray:
@ -83,11 +86,8 @@ class BaselineData(object):
return np.asarray(data) return np.asarray(data)
#if __name__ == "__main__": if __name__ == "__main__":
print("Test") dataset = Dataset(dataset_id='2011-06-14-ag')
embed() # dataset = Dataset(dataset_id='2018-11-09-aa-invivo-1')
exit() baseline = BaselineData(dataset)
embed()
dataset = Dataset(tuple=(Datasets & "dataset_id like '2018-11-09-aa-%'").fetch(limit=1, as_dict=True))
baseline = BaselineData(dataset)
embed()