API reference

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API reference#

Classes for general functionality#

datastructure_tools.utils.CreateDataStructureNew(path2proj, pipeline, Project, Experiment, sessionName, debug=True, overrule=False)#

debug - only print structure dont create pipeline has to contain a dict with keys like 0_raw with a list of folders to create

class datastructure_tools.utils.ElectrodePositionCalculator(atlas_path, target_point=None, insertion_point=None)#

Class to calculate the position of the electrode in the brain To get the coronal slice of the brain use get_coronal_slice To claculate points along electrode, target_point and insertion_point are needed

get_coronal_slice(ap, ml=0, dv=0)#

this function return the coronal slice of the point in mm

class datastructure_tools.utils.SessionClass(DB, test=False, *args, **kwargs)#

class abstracting all infos about the session can be reused in functions

Required inputs: DB - handle to DataBaseAccess animal_id -> str animal id in DB, will be checked session_datetime session_note -> str can be not provided project -> str project in DB, will be checked user -> str user in DB, will be checked expName -> str experiment name folder experiment_template -> str experiment_type name will be checked

probably new way to use it:

session = SessionClass(self.DB, animal_id=AnimalName2use, session_datetime=session_datetime,#

session_note=’This is a tutorial note’, project=’2020_testproject’,#

user=’tt1010’, expName=’totally_real_experiment’,#

experiment_template = ‘tutorial_experiment’, weight = ‘9999’, test = True)#

session.pushWholeSessionInfo2DB()#

old way to use it how to use:

session = SessionClass(self.DB, animal_id=AnimalName2use, session_datetime=session_datetime,#

session_note=self.Session_note.toPlainText(), project=self.Project_combo.currentText(),#

user=self.User_combo.currentText(), expName=self.ExpName_combo.currentText(),#

experiment_template = self.ExpType_combo.currentText(),test = BOOL if a test session)#

#pathcreationSuccess = session.createSession_path() # create Paths on server

TRUE if worked#

#PushSuccess = session.checkInputs() # checks inputs and pushes to DB

TRUE if worked#

#session.weight = float(self.AnimalWeightEdit.text()) #session.weight_note = self.WeightNoteEdit.text() #session.pushWeights()

pushWholeSessionInfo2DB(**kwargs)#

puts the session to DB with weights, Adds to Animalsheet entry and eLabFTW(both session entry and Animalsheet) use instead of checkInputs adn pushWeights all AnimalSheets fields to be entered should be pass as kwargs to the function eg.g pushSession2DB(housing=”Gruppe”,weiterleben=True .. etc.)

datastructure_tools.utils.add_row_to_animalsheet_df(current_animal_sheet, data_to_add, abbruchgewicht=None)#

takes a dataframe of an animal sheet and adds a row to that if abbruchgewicht is none: abbruchgewicht will be 0.8*weight

datastructure_tools.utils.change_animal_nr(DB, session_id: str, new_animal: str)#

function for renaming a Session if the animal id was wrongly entered, copies and renames the files as well :param DB: DataBaseAccess instance :param session_id: (str) session_id to be changed :param new_animal: (str) correct animal id

Returns:

datastructure_tools.utils.convert_date_from_animalsheet_back_to_pydate(animal_sheet_date, date_format=’%d/%m/%Y’)#

usage: pydate_obj = convert_date_back_to_pydate(animal_sheet.iloc[0][‘Datum und Wochentag’])

datastructure_tools.utils.create_probe_from_probeinterfacefile(path2file: str) -> (<class ‘list’>, <class ‘probeinterface.probe.Probe’>)#

This creates and add the corresponding probe from a probeinterface_file :param path2file: path 2 json file to be read in spike interface

  • Returns: list of dictionaries with electrode properties Probe file for plotting

datastructure_tools.utils.dict_to_uuid(key: dict)#

Given a dictionary key, returns a hash string as UUID :param key: Any python dictionary :type key: dict

datastructure_tools.utils.dict_to_uuid_my(key: dict)#

Given a dictionary key, returns a hash string as UUID this is better as it sorts nested dict

  • Parameters: key (dict) – Any python dictionary

datastructure_tools.utils.find_server_directory(root_directories: list) → Path#

Given multiple potential server directories, return correct root. Search and return one directory that is the parent of the given path. :param root_directories: potential root directories :type root_directories: list

  • Returns: root_directory (pathlib.Path object)

  • Raises: FileNotFoundError – No valid root directory

datastructure_tools.utils.get_Abbruchgewicht(DB, animal_id: str, weight_date: datetime) → float#

given animal_id and a datetime returns abbruchgewicht for this AnimalSheetEntry :param DB: DataBaseAccess instance :param animal_id: str :param weight_date: datetime of the entry in AnimalSheetEntry

  • Returns: Abbruchgewicht in g

  • Return type: float

datastructure_tools.utils.get_AbbruchgewichtList(DB, animal_id: str) → list#

given animal_id return a list of abbruchgewichte for each AnimalSheetEntry :param DB: DataBaseAccess instance :param animal_id: str

  • Returns: list

datastructure_tools.utils.json_serial(obj)#

JSON serializer for objects not serializable by default json code

datastructure_tools.utils.make_animalsheet_byanimal_id(DB, animal_id: str, savepath: [<class ‘str’>, <class ‘pathlib.Path’>] = None) → [<class ‘pathlib.Path’>, None]#

wrapper for the make_animalsheet_whole, without user mapping and signatures :param DB: DataBaseAccess instance :param animal_id: str animal_id :param savepath: optional path 2 save

  • Returns: path of the created animal_sheet

datastructure_tools.utils.remove_wd_fromentries(DB, animal_id: str)#

removes the WD from the procedure field of the animalsheet entry :param DB: DataBaseAccess instance :param animal_id: str of the animal id :return:

datastructure_tools.utils.sort_animalsheet_df_by_date(animal_sheet_to_sort)#

I guess there is an easier way to do this but here we are usage: sorted_animal_sheet = sort_animalsheet_by_date(animal_sheet)

classes to work with Surgery data, injections, implantation, etc. Autor: Artur

class datastructure_tools.Surgery_classes.ProbeImplant(**kwargs)#

this is not finished

show_on_atlas(ax=None)#

does Probe specific modifications plots the probeinterface plot

class datastructure_tools.Surgery_classes.WindowImplant(**kwargs)#

this is not finished

show_on_atlas(ax=None)#

does Lens specific modifications - the thickness of the lens

GUIs#

eLabFTW crawler#

class datastructure_tools.eLabFTW_api_utils.AnimalFields#

enum for fields in Animal in ELN

class datastructure_tools.eLabFTW_api_utils.FieldTypes#

this class enums the names for the different FieldTypes in eLabFTW

class datastructure_tools.eLabFTW_api_utils.PerfusionFields#

enum Class for the Perfusion Template in ELN

class datastructure_tools.eLabFTW_api_utils.VirusFields#

enum for fields for virus in ELN

class datastructure_tools.eLabFTW_api_utils.expStatus#

this class enums the names for the different experiment status in eLabFTW

datastructure_tools.eLabFTW_api_utils.get_fields_fromclass(cls) → list#

takes a class and returns list of the attributes of this class :param cls: the class to be checked

Returns: list of attributes

class datastructure_tools.eLabFTW_api_utils.itemStatus#

this class enums the names for the different itemStatus in eLabFTW

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