[frontend] improve finding, docstrings
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@ -4,7 +4,7 @@ import nixio as nix
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import os
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import numpy as np
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from IPython import embed
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from fishbook.backend.util import progress
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class Cell:
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def __init__(self, cell_id=None, tuple=None):
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@ -294,6 +294,9 @@ class Dataset:
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class RePro:
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"""Repro class represents an entry in the repro table. This is a run of a certain relacs "Research Protocol".
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"""
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def __init__(self, repro_id=None, tuple=None):
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if tuple:
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self.__tuple = tuple
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@ -349,24 +352,34 @@ class RePro:
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def stimuli(self):
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stims = Stimuli & "repro_id = '%s'" % self.id & "cell_id = '%s'" % self.cell_id
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return [Stimulus(tuple=s) for s in stims]
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@staticmethod
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def find(name=None, cell_id=None, cell_type=None, species=None, settings=None, quality=None):
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"""
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Cell type, quality, and species are ignored, if cell_id is provided
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:param repro_name:
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:param cell_id:
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:param cell_type:
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:param species:
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:param settings:
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:param quality:
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:return:
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def find(name=None, cell_id=None, cell_type=None, species=None, settings=[], quality=None, test=False):
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""" Finds Repro runs in the database. When called without arguments, all RePro runs are
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found and returned.
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Search can be narrowed by providing further search hints.
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**Note:** Cell type, quality, and species are ignored, if cell_id is provided
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**Note:** If there are many results fetching and creating objects may take a while. Consider running as test.
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Args:
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name (str, optional): The RePro name, or a part of it. Defaults to None.
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cell_id (str, optional): The cell_id. If given type, quality and species are ignored. Defaults to None.
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cell_type (str, optional): type of cell. Defaults to None.
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species (str, optional): The species name, or parts of it. Defaults to None.
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settings (list of string, optional): List of repro settings e.g. ["contrast: 20", "am: false"]. An AND connection is assumed. Defaults to None.
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quality (str, optional): The quality assessment. Defaults to None.
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test (bool, optional): defines whether or not the database matches should be fetched from the database.
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Returns:
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list of fishbook.RePro: list of results or empty list if test == True
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int: number of matches
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"""
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repros = Repros & True
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if name:
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repros = repros & "repro_name like '%{0:s}%'".format(name)
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if settings:
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repros = repros & "settings like '%{0:s}%'".format(settings)
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if len(settings) > 0:
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settings_pattern = " AND ".join(["settings like '%{0:s}%'".format(s) for s in settings])
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repros = repros & settings_pattern
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if cell_id:
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repros = repros & "cell_id = '{0:s}'".format(cell_id)
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if not cell_id and (cell_type or species or quality):
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@ -379,7 +392,15 @@ class RePro:
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cells = cells & "quality like '{0:s}'".format(quality)
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p = cells.proj("quality", "experimenter")
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repros = repros & p
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return [RePro(tuple=r) for r in repros]
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results = []
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total = len(repros)
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if not test:
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for i, r in enumerate(repros):
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results.append(RePro(tuple=r))
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progress(i+1, total, "fetching %i matches" % total)
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return results, total
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@property
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def _tuple(self):
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@ -456,27 +477,37 @@ class Stimulus:
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return self.__tuple.copy()
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@staticmethod
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def find(cell_id=None, repro_id=None, settings=None):
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def find(cell_id=None, repro_id=None, settings=[], test=False):
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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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settings (str, optional): [description]. Defaults to []].
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test (bool, optional): whether or not this is a test run. When true, results will not be fetched from the database. Defaults to False.
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Returns:
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List: of matching Stimulus presentations
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List: of matching Stimulus presentations, empty if test==True
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int: count of matches
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"""
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stimuli = Stimuli & True
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if 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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stimuli = stimuli & "repro_id = '{0:s}'".format(repro_id)
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if settings:
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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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if len(settings) > 0:
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settings_pattern = " AND ".join(["settings like '%{0:s}%'".format(s) for s in settings])
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stimuli = stimuli & settings_pattern
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results = []
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total = len(stimuli)
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if not test:
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for i, s in enumerate(stimuli):
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results.append(Stimulus(tuple=s))
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progress(i+1, total, "fetching %i matches" % total)
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return results, total
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class Subject:
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def __init__(self, subject_id=None, tuple=None):
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@ -516,7 +547,14 @@ class Subject:
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subjs = Subjects & True
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if species:
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subjs = (Subjects & "species like '%{0:s}%'".format(species))
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return [Subject(tuple=s) for s in subjs]
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results = []
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total = len(subjs)
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for i, s in enumerate(subjs):
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results.append(Subject(tuple=s))
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progress(i+1, total, "fetching %i matches" % total)
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return results, total
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@staticmethod
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def unique_species():
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