jgrewe/fishbook
2
1
Fork 1
Code Issues3 Pull Requests Releases Wiki Activity

Merge branch 'master' of https://whale.am28.uni-tuebingen.de/git/jgrewe/fishBook

Browse Source
This commit is contained in:
Jan Grewe 2020-08-03 18:26:50 +02:00
commit 5a4644344a
4 changed files with 13 additions and 7 deletions

BIN
docs/database_layout.mwb Normal file
View File

Binary file not shown.

BIN
docs/database_layout.png Normal file
View File

Binary file not shown.
Side by Side

After

(image error) Size: 111 KiB

0
fishbook/cmd/initialize.py Normal file
View File

20
fishbook/frontend/relacs_classes.py
View File

@ -27,7 +27,7 @@ class BaselineData:
def _get_data(self):
if not self.__dataset:
return
self.__repros = RePro.find("BaselineActivity", cell_id=self.__cell.id)
self.__repros, _ = RePro.find("BaselineActivity", cell_id=self.__cell.id)
for i in tqdm(range(len(self.__repros)), desc="loading data"):
r = self.__repros[i]
sd = self.__read_spike_data(r)
@ -311,7 +311,7 @@ class FIData:
def _get_data(self):
if not self.__dataset:
return
self.__repros = RePro.find("FICurve", cell_id=self.__cell.id)
self.__repros,_ = RePro.find("FICurve", cell_id=self.__cell.id)
for r in self.__repros:
sd, c, eods, time = self.__read_spike_data(r)
if sd is not None and len(sd) > 1:
@ -365,8 +365,8 @@ class FIData:
eods = []
time = []
contrasts = []
stimuli = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id)
if len(stimuli) == 0:
stimuli, count = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id)
if count == 0:
return spikes, contrasts, eods, time
data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
if not os.path.exists(data_source):
@ -376,7 +376,7 @@ class FIData:
b = f.blocks[0]
self.__all_spikes = b.data_arrays["Spikes-1"][:]
mt = None
for i in tqdm(range(len(stimuli)), desc="Loading data"):
for i in tqdm(range(count), desc="Loading data"):
s = stimuli[i]
if not mt or mt.id != s.multi_tag_id:
mt = b.multi_tags[s.multi_tag_id]
@ -539,12 +539,18 @@ class FIData:
class FileStimulusData:
"""The FileStimulus class provides access to the data recorded and the stimulus presented (if accessible)
during runs of the FileStimulus repro. Since the FileStimulus repro can put out any stimulus this class does not
provide any further analyses.
As any other relacs class it is instantiated with a Dataset entity.
"""
def __init__(self, dataset: Dataset):
"""
Constructor.
:param dataset: The dataset entity for which the filestimulus repro data should be loaded.
Args
fishbook.Dataset: The dataset entity for which the filestimulus repro data should be loaded.
"""
self.__spike_data = []
self.__contrasts = []
@ -557,7 +563,7 @@ class FileStimulusData:
def _get_data(self):
if not self.__dataset:
return
self.__repros = RePro.find("FileStimulus", cell_id=self.__cell.id)
self.__repros, _ = RePro.find("FileStimulus", cell_id=self.__cell.id)
for r in self.__repros:
sd, c, stims = self.__read_spike_data_from_nix(r) if self.__dataset.has_nix else self.__read_spike_data_from_directory(r)
if sd is not None and len(sd) > 1: