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

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Jan Grewe 2020-08-03 18:26:50 +02:00
commit 5a4644344a
4 changed files with 13 additions and 7 deletions
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fishbook/cmd/initialize.py Normal file
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fishbook/frontend/relacs_classes.py
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@ -27,7 +27,7 @@ class BaselineData:
def _get_data(self): def _get_data(self):
if not self.__dataset: if not self.__dataset:
return 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"): for i in tqdm(range(len(self.__repros)), desc="loading data"):
r = self.__repros[i] r = self.__repros[i]
sd = self.__read_spike_data(r) sd = self.__read_spike_data(r)
@ -311,7 +311,7 @@ class FIData:
def _get_data(self): def _get_data(self):
if not self.__dataset: if not self.__dataset:
return 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: for r in self.__repros:
sd, c, eods, time = self.__read_spike_data(r) sd, c, eods, time = self.__read_spike_data(r)
if sd is not None and len(sd) > 1: if sd is not None and len(sd) > 1:
@ -365,8 +365,8 @@ class FIData:
eods = [] eods = []
time = [] time = []
contrasts = [] contrasts = []
stimuli = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id) stimuli, count = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id)
if len(stimuli) == 0: if count == 0:
return spikes, contrasts, eods, time return spikes, contrasts, eods, time
data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix") data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
if not os.path.exists(data_source): if not os.path.exists(data_source):
@ -376,7 +376,7 @@ class FIData:
b = f.blocks[0] b = f.blocks[0]
self.__all_spikes = b.data_arrays["Spikes-1"][:] self.__all_spikes = b.data_arrays["Spikes-1"][:]
mt = None mt = None
for i in tqdm(range(len(stimuli)), desc="Loading data"): for i in tqdm(range(count), desc="Loading data"):
s = stimuli[i] s = stimuli[i]
if not mt or mt.id != s.multi_tag_id: if not mt or mt.id != s.multi_tag_id:
mt = b.multi_tags[s.multi_tag_id] mt = b.multi_tags[s.multi_tag_id]
@ -539,12 +539,18 @@ class FIData:
class FileStimulusData: 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): def __init__(self, dataset: Dataset):
""" """
Constructor. 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.__spike_data = []
self.__contrasts = [] self.__contrasts = []
@ -557,7 +563,7 @@ class FileStimulusData:
def _get_data(self): def _get_data(self):
if not self.__dataset: if not self.__dataset:
return 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: 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) 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: if sd is not None and len(sd) > 1: