fixes and docstring stubs
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@ -1,4 +1,4 @@
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from .database.database import Cells, Datasets, CellDatasetMap, Subjects, SubjectProperties, SubjectDatasetMap, Stimuli, Repros
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from fishbook.database.database import Cells, Datasets, CellDatasetMap, Subjects, SubjectProperties, SubjectDatasetMap, Stimuli, Repros
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import nixio as nix
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import os
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import numpy as np
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@ -57,7 +57,7 @@ class Cell:
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@property
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def datasets(self):
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return [Dataset(tuple=d) for d in (Datasets & (CellDatasetMap & self.id)).fetch(as_dict=True)]
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return [Dataset(tuple=d) for d in (Datasets & (CellDatasetMap & {"cell_id": self.id})).fetch(as_dict=True)]
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@property
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def repro_runs(self):
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@ -90,7 +90,15 @@ class Cell:
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class Dataset:
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"""[summary]
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"""
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def __init__(self, dataset_id=None, tuple=None):
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"""[summary]
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Args:
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dataset_id ([type], optional): [description]. Defaults to None.
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tuple ([type], optional): [description]. Defaults to None.
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"""
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self.__samplerate = 0.0
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if tuple:
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self.__tuple = tuple
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@ -106,10 +114,20 @@ class Dataset:
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@property
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def id(self):
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"""The id of the dataset.
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Returns:
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str: the id
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"""
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return self.__tuple["dataset_id"]
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@property
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def experimenter(self):
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"""The person who recording the dataset.
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Returns:
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str: The experimenter
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"""
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return self.__tuple["experimenter"]
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@property
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@ -142,13 +160,13 @@ class Dataset:
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@property
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def cells(self):
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cs = (Cells * (CellDatasetMap & self.__tuple))
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return [Cell(tuple=c) for c in cs]
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cell_list = (Cells * (CellDatasetMap & self.__tuple))
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return [Cell(tuple=c) for c in cell_list]
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@property
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def subjects(self):
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subjs = (Subjects * (SubjectDatasetMap & self.__tuple))
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return [Subject(tuple=s) for s in subjs]
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subject_list = (Subjects * (SubjectDatasetMap & self.__tuple))
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return [Subject(tuple=s) for s in subject_list]
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@property
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def samplerate(self):
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@ -156,14 +174,14 @@ class Dataset:
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@staticmethod
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def find(min_duration=None, experimenter=None, quality=None):
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dsets = Datasets
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dataset_list = Datasets
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if min_duration:
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dsets = dsets & "duration > %.2f" % min_duration
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dataset_list = dataset_list & "duration > %.2f" % min_duration
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if experimenter:
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dsets = dsets & "experimenter like '%{0:s}%'".format(experimenter)
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dataset_list = dataset_list & "experimenter like '%{0:s}%'".format(experimenter)
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if quality:
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dsets = dsets & "quality like '{0:s}'".format(quality)
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return [Dataset(tuple=d) for d in dsets]
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dataset_list = dataset_list & "quality like '{0:s}'".format(quality)
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return [Dataset(tuple=d) for d in dataset_list]
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def __find_samplerate(self, trace_name="V-1"):
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if self.has_nix and os.path.exists(os.path.join(self.data_source, self.id, '.nix')):
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@ -174,16 +192,16 @@ class Dataset:
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if trace.dimensions[0].dimension_type == nix.DimensionType.Sample:
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self.__samplerate = 1./trace.dimensions[0].sampling_interval
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else:
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print("Requested trace %s has no sampled dimension!" % s)
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print("Requested trace %s has no sampled dimension!" % trace_name)
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else:
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print("Requested trace %s was not found!" % s)
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print("Requested trace %s was not found!" % trace_name)
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f.close()
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else:
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stim_file = os.path.join(self.data_source , 'stimuli.dat')
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if not os.path.exists(stim_file):
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stimulus_file = os.path.join(self.data_source , 'stimuli.dat')
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if not os.path.exists(stimulus_file):
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return
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lines = None
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with open(stim_file, 'r') as f:
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with open(stimulus_file, 'r') as f:
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lines = f.readlines()
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for l in lines:
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if "sample interval1" in l:
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@ -290,13 +308,16 @@ class RePro:
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class Stimulus:
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"""The stimulus class represents a Stimulus that was presented. A Stimulus has several properties
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such as the start time, the duarion
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"""
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def __init__(self, stimulus_id=None, tuple=None):
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if tuple:
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self.__tuple = tuple
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elif stimulus_id:
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stims = Stimuli & "stimulus_id = '%s'" %stimulus_id
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_results_check(stims, stimulus_id, "Stimulus ID")
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self.__tuple = stims.fetch(limit=1, as_dict=True)[0]
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stimuli = Stimuli & "stimulus_id = '%s'" %stimulus_id
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_results_check(stimuli, stimulus_id, "Stimulus ID")
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self.__tuple = stimuli.fetch(limit=1, as_dict=True)[0]
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else:
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print("Empty RePro, not linked to any database entry!")
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@ -339,10 +360,6 @@ class Stimulus:
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def multi_tag_id(self):
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return self.__tuple["mtag_id"]
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@property
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def settings(self):
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return self.__tuple["settings"]
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@property
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def run(self):
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return self.__tuple["run"]
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@ -351,7 +368,6 @@ class Stimulus:
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def index(self):
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return self.__tuple["stimulus_index"]
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@property
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def settings(self):
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return _safe_get_val(self.__tuple, "settings", "")
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@ -362,14 +378,25 @@ class Stimulus:
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@staticmethod
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def find(cell_id=None, repro_id=None, settings=None):
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stims = Stimuli & True
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"""Find stimulus presentations that match in certain properties.
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Examples:
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Args:
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cell_id (str, optional): [description]. Defaults to None.
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repro_id (str, optional): [description]. Defaults to None.
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settings (str, optional): [description]. Defaults to None.
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Returns:
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List: of matching Stimulus presentations
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"""
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stimuli = Stimuli & True
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if cell_id:
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stims = stims & "cell_id = '{0:s}'".format(cell_id)
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stimuli = stimuli & "cell_id = '{0:s}'".format(cell_id)
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if repro_id:
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stims = stims & "repro_id = '{0:s}'".format(repro_id)
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stimuli = stimuli & "repro_id = '{0:s}'".format(repro_id)
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if settings:
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stims = stims & "settings like '%{0:s}%'".format(settings)
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return [Stimulus(tuple=s) for s in stims]
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stimuli = stimuli & "settings like '%{0:s}%'".format(settings)
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return [Stimulus(tuple=s) for s in stimuli]
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class Subject:
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