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rearraning things

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This commit is contained in:
Jan Grewe 2020-07-22 13:35:12 +02:00
parent 1874985f56
commit 14bed0cc6a
6 changed files with 35 additions and 36 deletions
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8
fishbook/__init__.py
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@ -1,4 +1,4 @@
from .fishbook import Cell, Subject, Stimulus, Dataset, RePro from fishbook.frontend.frontend_classes import Cell, Subject, Stimulus, Dataset, RePro
import fishbook.reproclasses as repros #import fishbook.reproclasses as repros
import fishbook.database as database #import fishbook.database as database
__all__ = ['fishbook', 'database'] __all__ = ['', '']

3
fishbook/backend/__init__.py
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@ -1,3 +1,2 @@
from .database import * from .database import Cells, Datasets, Stimuli, Repros, Subjects, SubjectDatasetMap, CellDatasetMap
__all__ = ['database'] __all__ = ['database']

1
fishbook/frontend/__init__.py Normal file
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@ -0,0 +1 @@
# __all__ = ["fronten_classes", "reproclasses"]

48
fishbook/frontend/fishbook.py → fishbook/frontend/frontend_classes.py
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@ -1,21 +1,11 @@
from fishbook.database.database import Cells, Datasets, CellDatasetMap, Subjects, SubjectProperties, SubjectDatasetMap, Stimuli, Repros from fishbook.backend.database import Cells, Datasets, CellDatasetMap, Subjects, SubjectProperties, SubjectDatasetMap, Stimuli, Repros
from .util import safe_get_val, results_check
import nixio as nix import nixio as nix
import os import os
import numpy as np import numpy as np
from IPython import embed from IPython import embed
def _safe_get_val(dictionary:dict, key, default=None):
return dictionary[key] if key in dictionary.keys() else default
def _results_check(results, id, text="ID"):
if len(results) == 0:
raise ValueError("%s %s does not exist!" % (text, id))
elif len(results) > 1:
raise ValueError("%s %s is not unique!" % (text, id))
class Cell: class Cell:
def __init__(self, cell_id=None, tuple=None): def __init__(self, cell_id=None, tuple=None):
if tuple: if tuple:
@ -23,7 +13,7 @@ class Cell:
elif cell_id: elif cell_id:
pattern = "cell_id like '{0:s}'".format(cell_id) pattern = "cell_id like '{0:s}'".format(cell_id)
cells = (Cells & pattern) cells = (Cells & pattern)
_results_check(cells, cell_id, "Cell ID") results_check(cells, cell_id, "Cell ID")
self.__tuple = cells.fetch(as_dict=True)[0] self.__tuple = cells.fetch(as_dict=True)[0]
else: else:
print("Empty Cell, not linked to any database entry!") print("Empty Cell, not linked to any database entry!")
@ -105,7 +95,7 @@ class Dataset:
elif dataset_id: elif dataset_id:
pattern = "dataset_id like '{0:s}'".format(dataset_id) pattern = "dataset_id like '{0:s}'".format(dataset_id)
dsets = (Datasets & pattern) dsets = (Datasets & pattern)
_results_check(dsets, dataset_id, "Dataset ID") results_check(dsets, dataset_id, "Dataset ID")
self.__tuple = dsets.fetch(limit=1, as_dict=True)[0] self.__tuple = dsets.fetch(limit=1, as_dict=True)[0]
else: else:
print("Empty dataset, not linked to any database entry!") print("Empty dataset, not linked to any database entry!")
@ -220,7 +210,7 @@ class RePro:
self.__tuple = tuple self.__tuple = tuple
elif repro_id: elif repro_id:
repros = (RePro & "repro_id like '{0:s}'".format(repro_id)) repros = (RePro & "repro_id like '{0:s}'".format(repro_id))
_results_check(repros, repro_id, "RePro ID") results_check(repros, repro_id, "RePro ID")
self.__tuple = repros.fetch(limit=1, as_dict=True)[0] self.__tuple = repros.fetch(limit=1, as_dict=True)[0]
else: else:
self.__tuple = {} self.__tuple = {}
@ -228,15 +218,15 @@ class RePro:
@property @property
def id(self): def id(self):
return _safe_get_val(self.__tuple, "repro_id", "") return safe_get_val(self.__tuple, "repro_id", "")
@property @property
def run(self): def run(self):
return _safe_get_val(self.__tuple, "run", -1) return safe_get_val(self.__tuple, "run", -1)
@property @property
def cell_id(self): def cell_id(self):
return _safe_get_val(self.__tuple, "cell_id", "") return safe_get_val(self.__tuple, "cell_id", "")
@property @property
def cell(self): def cell(self):
@ -252,19 +242,19 @@ class RePro:
@property @property
def name(self): def name(self):
return _safe_get_val(self.__tuple, "repro_name", "") return safe_get_val(self.__tuple, "repro_name", "")
@property @property
def settings(self): def settings(self):
return _safe_get_val(self.__tuple, "settings", "") return safe_get_val(self.__tuple, "settings", "")
@property @property
def start(self): def start(self):
return _safe_get_val(self.__tuple, "start", 0.0) return safe_get_val(self.__tuple, "start", 0.0)
@property @property
def duration(self): def duration(self):
return _safe_get_val(self.__tuple, "duration", 0.0) return safe_get_val(self.__tuple, "duration", 0.0)
@property @property
def stimuli(self): def stimuli(self):
@ -316,16 +306,16 @@ class Stimulus:
self.__tuple = tuple self.__tuple = tuple
elif stimulus_id: elif stimulus_id:
stimuli = Stimuli & "stimulus_id = '%s'" %stimulus_id stimuli = Stimuli & "stimulus_id = '%s'" %stimulus_id
_results_check(stimuli, stimulus_id, "Stimulus ID") results_check(stimuli, stimulus_id, "Stimulus ID")
self.__tuple = stimuli.fetch(limit=1, as_dict=True)[0] self.__tuple = stimuli.fetch(limit=1, as_dict=True)[0]
else: else:
print("Empty RePro, not linked to any database entry!") print("Empty RePro, not linked to any database entry!")
def __str__(self): def __str__(self):
str = "Stimulus %s: " % _safe_get_val(self.__tuple, "stimulus_id", "") str = "Stimulus %s: " % safe_get_val(self.__tuple, "stimulus_id", "")
str += "\nStart time/index: %0.4f/%i, duration: %.3f" % (_safe_get_val(self.__tuple, "start_time", 0.0), str += "\nStart time/index: %0.4f/%i, duration: %.3f" % (safe_get_val(self.__tuple, "start_time", 0.0),
_safe_get_val(self.__tuple, "start_index", -1), safe_get_val(self.__tuple, "start_index", -1),
_safe_get_val(self.__tuple, "duration", 0.0)) safe_get_val(self.__tuple, "duration", 0.0))
return str return str
@property @property
@ -370,7 +360,7 @@ class Stimulus:
@property @property
def settings(self): def settings(self):
return _safe_get_val(self.__tuple, "settings", "") return safe_get_val(self.__tuple, "settings", "")
@property @property
def _tuple(self): def _tuple(self):
@ -405,7 +395,7 @@ class Subject:
self.__tuple = tuple self.__tuple = tuple
elif subject_id: elif subject_id:
subjects = Subjects & "subject_id like '{0:s}'".format(subject_id) subjects = Subjects & "subject_id like '{0:s}'".format(subject_id)
_results_check(subjects, subject_id, "Subject ID") results_check(subjects, subject_id, "Subject ID")
self.__tuple = subjects.fetch()[0] self.__tuple = subjects.fetch()[0]
else: else:
self.__tuple = {} self.__tuple = {}

0
fishbook/frontend/reproclasses.py → fishbook/frontend/relacs_classes.py
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9
fishbook/frontend/util.py Normal file
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@ -0,0 +1,9 @@
def safe_get_val(dictionary:dict, key, default=None):
return dictionary[key] if key in dictionary.keys() else default
def results_check(results, id, text="ID"):
if len(results) == 0:
raise ValueError("%s %s does not exist!" % (text, id))
elif len(results) > 1:
raise ValueError("%s %s is not unique!" % (text, id))