Source code for autopilot.prefs

Module to hold module-global variables as preferences.

Upon import, prefs attempts to import a ``prefs.json`` file from the default location (see :func:`.prefs.init` ).

Prefs are then accessed with :func:`.prefs.get` and :func:`.prefs.set` functions. After initialization, if a pref if ``set``,
it is stored in the ``prefs.json`` file -- prefs are semi-durable and persist across sessions.

When attempting to get a pref that is not set, :func:`.prefs.get` will first try to find a default value (set in
:data:`._PREFS` , and if none is found return ``None`` -- accordingly
no prefs should be intentionally set to None, as it signifies that the pref is not set.

Prefs are thread- and process-safe, as they are stored and served by a :class:`multiprocessing.Manager` object.

``prefs.json`` is typically generated by running :mod:`autopilot.setup.setup_autopilot` , though you can freestyle it
if you are so daring.

The **``HARDWARE``** pref is a little special. It specifies how each of the :mod:`.hardware` components connected to the system
is configured. It is a dictionary with this general structure::

    'HARDWARE': {
        'GROUP': {
            'ID': {
                'hardware_arg': 'val'

where there are user-named ``'GROUPS'`` of hardware objects, like ``'LEDS'`` , etc. Within a group, each object has its
``'ID'`` (passed as the ``name`` argument to the hardware initialization method) which allows it to be identified from
the other components in the group. The intention of this structure is to allow multiple categories of hardware objects
to be parameterized and used separately, even though they might be the same object type. Eg. we may have three LEDs
in our nosepokes, but also have an LED that serves at the arena light. If we wanted to write a command that turns off all
LEDs, we would have to explicitly specify their IDs, making it difficult to re-use very common hardware command patterns
within tasks. There are obvious drawbacks to this scheme -- clunky, ambiguous, etc. and will be deprecated as parameterization
continues to congeal across the library.

The class that each element is used with is determined by the :attr:`.Task.HARDWARE`
dictionary. Specifically, the :meth:`.Task.init_hardware` method does something like::

    self.hardware['GROUP']['ID'] = self.HARDWARE['GROUP']['ID'](**prefs.get('HARDWARE')['GROUP']['ID'])

    These are **not** hard coded prefs. :data:`_DEFAULTS` populates the *default* values for prefs, but local prefs are
    always restored from and saved to ``prefs.json`` . If you're editing this file and things aren't changing,
    you're in the wrong place!

This iteration of prefs with respect to work done on the `People's Ventilator Project <>`_

If a pref has a string for a ``'deprecation'`` field in :data:`.prefs._DEFAULTS` , a ``FutureWarning``
will be raised with the string given as the message


# this is strictly a placeholder module to
# allow global access to prefs without explicit passing.
# DO NOT hardcode prefs here. only add placeholder values for certain 'universal' params
# A prefs.json file should be generated with an appropriate setup routine
# (see setup dir)
# then you should call prefs.init(prefs.json) if the if __name__=="__main__" block

# Prefs is a top-level module! It shouldn't depend on anything else in Autopilot,
# and if it does, it should carefully import it where it is needed!
# (prefs needs to be possible to import everywhere, including eg. in setup_autopilot)
import json
import subprocess
import multiprocessing as mp
from threading import Lock
import os
import logging
import typing
import sys
import types
from pathlib import Path
from ctypes import c_bool
from enum import Enum, auto
import warnings

#from autopilot.core.loggers import init_logger
from collections import OrderedDict as odict
from autopilot.exceptions import DefaultPrefWarning

[docs]class Scopes(Enum): """ Enum that lists available scopes and groups for prefs Scope can be an agent type, common (for everyone), or specify some subgroup of prefs that should be presented together (like directories) COMMON = All Agents DIRECTORY = Prefs group for specifying directory structure TERMINAL = prefs for Terminal Agents Pilot = Prefs for Pilot agents LINEAGE = prefs for networking lineage (until networking becomes more elegant ;) AUDIO = Prefs for configuring the Jackd audio server """ COMMON = auto() #: All agents TERMINAL = auto() #: Prefs specific to Terminal Agents PILOT = auto() #: Prefs specific to Pilot Agents DIRECTORY = auto() #: Directory structure LINEAGE = auto() #: Prefs for coordinating network between pilots and children AUDIO = auto() #: Audio prefs...
using_manager = False if getattr(mp.process.current_process(), '_inheriting', False): # Check if it's safe to use multiprocessing manager, using the check in multiprocessing/ # see _PREF_MANAGER = None _PREFS = {} _INITIALIZED = False _LOCK = Lock() else: try: _PREF_MANAGER = mp.Manager() # type: typing.Optional[mp.managers.SyncManager] """ The :class:`multiprocessing.Manager` that stores prefs during system operation and makes them available and consistent across processes. """ using_manager = True _PREFS = _PREF_MANAGER.dict() # type: mp.managers.SyncManager.dict """ stores a dictionary of preferences that mirrors the global variables. """ _INITIALIZED = mp.Value(c_bool, False) # type: mp.Value """ Boolean flag to indicate whether prefs have been initialzied from ``prefs.json`` """ _LOCK = mp.Lock() # type: mp.Lock """ :class:`multiprocessing.Lock` to control access to ``prefs.json`` """ except (EOFError, FileNotFoundError): # can't use mp.Manager in ipython and other interactive contexts # fallback to just regular old dict _PREF_MANAGER = None _PREFS = {} _INITIALIZED = False _LOCK = Lock() _LOGGER = None # type: typing.Union[logging.Logger, None] """ Logger used by prefs initialized by :func:`.core.loggers.init_logger` Initially None, created once prefs are populated because init_logger requires some prefs to be set (uh the logdir and level and stuff) """ # not documenting, just so that the full function doesn't need to be put in for each directory # lol at this literal reanimated fossil halfway evolved between os.path and pathlib _basedir = Path(os.path.join(os.path.expanduser("~"), "autopilot")) _DEFAULTS = odict({ 'NAME': { 'type': 'str', "text": "Agent Name:", "scope": Scopes.COMMON }, 'PUSHPORT': { 'type': 'int', "text": "Push Port - Router port used by the Terminal or upstream agent:", "default": "5560", "scope": Scopes.COMMON }, 'MSGPORT': { 'type': 'int', "text": "Message Port - Router port used by this agent to receive messages:", "default": "5565", "scope": Scopes.COMMON }, 'TERMINALIP': { 'type': 'str', "text": "Terminal IP:", "default": "", "scope": Scopes.COMMON }, 'LOGLEVEL': { 'type': 'choice', "text": "Log Level:", "choices": ("DEBUG", "INFO", "WARNING", "ERROR"), "default": "WARNING", "scope": Scopes.COMMON }, 'LOGSIZE': { 'type': 'int', "text": "Size of individual log file (in bytes)", "default": 5 * (2 ** 20), # 50MB "scope": Scopes.COMMON }, 'LOGNUM': { 'type': 'int', "text": "Number of logging backups to keep of LOGSIZE", "default": 4, "scope": Scopes.COMMON }, # 4 * 5MB = 20MB per module 'CONFIG': { 'type': 'list', "text": "System Configuration", 'hidden': True, "scope": Scopes.COMMON }, 'VENV': { 'type': 'str', 'text': 'Location of virtual environment, if used.', "scope": Scopes.COMMON, "default": str(Path(sys.prefix).resolve()) if hasattr(sys, 'real_prefix') or (sys.base_prefix != sys.prefix) else False }, 'AUTOPLUGIN': { 'type': 'bool', 'text': "Attempt to import the contents of the plugin directory", "scope": Scopes.COMMON, "default": True }, 'PLUGIN_DB': { 'type': 'str', 'text': 'filename to use for the .json plugin_db that keeps track of installed plugins', "default": str(_basedir / "plugin_db.json"), "scope": Scopes.COMMON }, 'BASEDIR': { 'type': 'str', "text": "Base Directory", "default": str(_basedir), "scope": Scopes.DIRECTORY }, 'DATADIR': { 'type': 'str', "text": "Data Directory", "default": str(_basedir / 'data'), "scope": Scopes.DIRECTORY }, 'SOUNDDIR': { 'type': 'str', "text": "Sound file directory", "default": str(_basedir / 'sounds'), "scope": Scopes.DIRECTORY }, 'LOGDIR': { 'type': 'str', "text": "Log Directory", "default": str(_basedir / 'logs'), "scope": Scopes.DIRECTORY }, 'VIZDIR': { 'type': 'str', "text": "Directory to store Visualization results", "default": str(_basedir / 'viz'), "scope": Scopes.DIRECTORY }, 'PROTOCOLDIR': { 'type': 'str', "text": "Protocol Directory", "default": str(_basedir / 'protocols'), "scope": Scopes.DIRECTORY }, 'PLUGINDIR': { 'type': 'str', "text": "Directory to import ", "default": str(_basedir / 'plugins'), "scope": Scopes.DIRECTORY }, 'REPODIR': { 'type': 'str', 'text': 'Location of Autopilot repo/library', 'default': Path(__file__).resolve().parents[1], "scope": Scopes.DIRECTORY }, 'CALIBRATIONDIR': { 'type': 'str', 'text': 'Location of calibration files for solenoids, etc.', 'default': str(_basedir / 'calibration'), 'scope': Scopes.DIRECTORY }, 'PIGPIOMASK': { 'type': 'str', 'text': 'Binary mask controlling which pins pigpio controls according to their BCM numbering, see the -x parameter of pigpiod', 'default': "1111110000111111111111110000", "scope": Scopes.PILOT }, 'PIGPIOARGS': { 'type': 'str', 'text': 'Arguments to pass to pigpiod on startup', 'default': '-t 0 -l', "scope": Scopes.PILOT }, 'PULLUPS': { 'type': 'list', 'text': 'Pins to pull up on system startup? (list of form [1, 2])', "scope": Scopes.PILOT }, 'PULLDOWNS': { 'type': 'list', 'text': 'Pins to pull down on system startup? (list of form [1, 2])', "scope": Scopes.PILOT }, 'PING_INTERVAL': { 'type': 'float', 'text': 'How many seconds should pilots wait in between pinging the Terminal?', 'default': 5, 'scope': Scopes.PILOT }, 'DRAWFPS': { 'type': 'int', "text": "FPS to draw videos displayed during acquisition", "default": "20", "scope": Scopes.TERMINAL }, 'PILOT_DB': { 'type': 'str', 'text': "filename to use for the .json pilot_db that maps pilots to subjects (relative to BASEDIR)", "default": str(_basedir / "pilot_db.json"), "scope": Scopes.TERMINAL }, 'TERMINAL_SETTINGS_FN':{ 'type': 'str', 'text': 'filename to store QSettings file for Terminal', 'default': str(_basedir / "terminal.conf"), "scope": Scopes.TERMINAL }, 'TERMINAL_WINSIZE_BEHAVIOR': { 'type': 'choice', 'text': 'Strategy for resizing terminal window on opening', "choices": ('remember', 'moderate', 'maximum', 'custom'), "default": "remember", "scope": Scopes.TERMINAL }, 'TERMINAL_CUSTOM_SIZE': { 'type': 'list', 'text': 'Custom size for window, specified as [px from left, px from top, width, height]', 'default': [0, 0, 1000, 400], 'depends': ('TERMINAL_WINSIZE_BEHAVIOR', 'custom'), 'scope': Scopes.TERMINAL }, 'LINEAGE': { 'type': 'choice', "text": "Are we a parent or a child?", "choices": ("NONE", "PARENT", "CHILD"), "scope": Scopes.LINEAGE }, 'CHILDID': { 'type': 'list', "text": "List of Child ID:", 'default': [], "depends": ("LINEAGE", "PARENT"), "scope": Scopes.LINEAGE }, 'PARENTID': { 'type': 'str', "text": "Parent ID:", "depends": ("LINEAGE", "CHILD"), "scope": Scopes.LINEAGE }, 'PARENTIP': { 'type': 'str', "text": "Parent IP:", "depends": ("LINEAGE", "CHILD"), "scope": Scopes.LINEAGE }, 'PARENTPORT': { 'type': 'str', "text": "Parent Port:", "depends": ("LINEAGE", "CHILD"), "scope": Scopes.LINEAGE }, 'AUDIOSERVER': { 'type': 'bool', 'text': 'Enable jack audio server?', "scope": Scopes.AUDIO }, 'NCHANNELS': { 'type': 'int', 'text': "Number of Audio channels (deprecated; used OUTCHANNELS)", 'default': 1, 'depends': 'AUDIOSERVER', "scope": Scopes.AUDIO, 'deprecation': "Deprecated and will be removed, use OUTCHANNELS instead" }, 'OUTCHANNELS': { 'type': 'list', 'text': 'List of Audio channel indexes to connect to', 'default': '', 'depends': 'AUDIOSERVER', "scope": Scopes.AUDIO }, 'FS': { 'type': 'int', 'text': 'Audio Sampling Rate', 'default': 192000, 'depends': 'AUDIOSERVER', "scope": Scopes.AUDIO }, 'ALSA_NPERIODS': { 'type': 'int', 'text': 'number of buffer periods to use with ALSA sound driver', 'default': 3, 'depends': 'AUDIOSERVER', 'scope': Scopes.AUDIO }, 'JACKDSTRING': { 'type': 'str', 'text': 'Arguments to pass to jackd, see the jackd manpage', 'default': 'jackd -P75 -p16 -t2000 -dalsa -dhw:sndrpihifiberry -P -rfs -nper -s &', 'depends': 'AUDIOSERVER', "scope": Scopes.AUDIO }, }) """ Ordered Dictionary containing default values for prefs. An Ordered Dictionary lets the prefs be displayed in gui elements in a predictable order, but prefs are stored in ``prefs.json`` in alphabetical order and the 'live' prefs used during runtime are stored in :data:`._PREFS` Each entry should be a dict with the following structure:: "PREF_NAME": { "type": (str, int, bool, choice, list) # specify the appropriate GUI input, str or int are validators, choices are a # dropdown box, and lists allow users to specify lists of values like "[0, 1]" "default": If possible, assign default value, otherwise None "text": human-readable text that described the pref "scope": to whom does this pref apply? see :class:`.Scopes` "depends": name of another pref that needs to be supplied/enabled for this one to be enabled (eg. don't set sampling rate of audio server if audio server disabled) can also be specified as a tuple like ("LINEAGE", "CHILD") that enables the option when prefs[depends[0]] == depends[1] "choices": If type=="choice", a tuple of available choices. } """ _WARNED = [] """ Keep track of which prefs we have warned about getting defaults for so we don't warn a zillion times """
[docs]def get(key: typing.Union[str, None] = None): """ Get a pref! If a value for the given ``key`` can't be found, prefs will attempt to Args: key (str, None): get pref of specific ``key``, if ``None``, return all prefs Returns: value of pref (type variable!), or ``None`` if no pref of passed ``key`` """ # if nothing is requested of us, return everything if key is None: if using_manager: return globals()['_PREFS']._getvalue() else: return globals()['_PREFS'].copy() else: # check for deprecation dep_notice = globals()['_DEFAULTS'].get(key, {}).get('deprecation', None) if dep_notice is not None: warnings.warn(dep_notice, FutureWarning) # try to get the value from the prefs manager try: # if it's a directory and it doesn't exist, try and make it if globals()['_DEFAULTS'].get(key, {}).get('scope', False) == Scopes.DIRECTORY: try: path = Path(globals()['_PREFS'][key]).resolve() if not path.exists(): path.mkdir(parents=True, exist_ok=True) except Exception as e: warnings.warn(f"prefs {key} was a directory, but a directory couldnt be created. got exception {e}") return globals()['_PREFS'][key] # if none exists... except KeyError: # try to get a default value try: default_val = globals()['_DEFAULTS'][key]['default'] if key not in globals()['_WARNED']: globals()['_WARNED'].append(key) warnings.warn(f'Returning default prefs value {key} : {default_val} (ideally this shouldnt happen and everything should be specified in prefs', DefaultPrefWarning) return default_val # if you still can't find a value, None is an unambiguous signal for pref not set # (no pref is ever None) except KeyError: return None
[docs]def set(key: str, val): """ Set a pref! Note: Whenever a pref is set, the prefs file is automatically updated -- prefs are system-durable!! (specifically, whenever the module-level ``_INITIALIZED`` value is set to True, prefs are saved to file to avoid overwriting before loading) Args: key (str): Name of pref to set val: Value of pref to set (prefs are not type validated against default types) """ globals()['_PREFS'][key] = val if using_manager: initialized = globals()['_INITIALIZED'].value else: initialized = globals()['_INITIALIZED'] if initialized and 'pytest' not in sys.modules: save_prefs()
[docs]def save_prefs(prefs_fn: str = None): """ Dump prefs into the ``prefs_fn`` .json file Args: prefs_fn (str, None): if provided, pathname to ``prefs.json`` otherwise resolve ``prefs.json`` according the to the normal methods.... """ if prefs_fn is None: try: prefs_fn = str(Path(get('BASEDIR')) / 'prefs.json') except KeyError: raise RuntimeError('Asked to save prefs without BASEDIR being set -- indicative of prefs being saved ' 'before initialized') # take lock for access to prefs file with globals()['_LOCK']: with open(prefs_fn, 'w') as prefs_f: if using_manager: save_prefs = globals()['_PREFS']._getvalue() else: save_prefs = globals()['_PREFS'].copy() json.dump(save_prefs, prefs_f, indent=4, separators=(',', ': '))
[docs]def init(fn=None): """ Initialize prefs on autopilot start. If passed dict of prefs or location of prefs.json, load and use that Otherwise - Look for the autopilot wayfinder ``~/.autopilot`` file that tells us where the user directory is - look in default location ``~/autopilot/prefs.json`` Todo: This function may be deprecated in the future -- in its current form it serves to allow the sorta janky launch methods in the headers/footers of autopilot/core/ and autopilot/core/ that will eventually be transformed into a unified agent framework to make launching easier. Ideally one would be able to just import prefs without having to explicitly initialize it, but we need to formalize the full launch process before we make the full lurch to that model. Args: fn (str, dict): a path to `prefs.json` or a dictionary of preferences """ if isinstance(fn, str): with open(fn, 'r') as pfile: prefs = json.load(pfile) elif isinstance(fn, dict): prefs = fn elif fn is None: # try to load from default location autopilot_wayfinder = os.path.join(os.path.expanduser('~'), '.autopilot') if os.path.exists(autopilot_wayfinder): with open(autopilot_wayfinder, 'r') as wayfinder_f: fn = os.path.join(, 'prefs.json') else: fn = os.path.join(os.path.expanduser('~'), 'autopilot', 'prefs.json') if not os.path.exists(fn): # tried to load defaults, return quietly return with open(fn, 'r') as pfile: prefs = json.load(pfile) # Get the current git hash if prefs.get('REPODIR', False): try: prefs['HASH'] = git_version(prefs.get('REPODIR')) except Exception as e: prefs['HASH'] = '' warnings.warn(f'git hash for repo could not be found! will not be able to keep good provenance! got exception: \n{e}') else: warnings.warn('REPODIR is not set in prefs.json, cant get git hash!!!') # FIXME: This 100% should not happen here and should happen in the relevant hardware classes. # Load any calibration data if prefs.get('BASEDIR', False): cal_path = os.path.join(prefs['BASEDIR'], 'port_calibration_fit.json') cal_raw = os.path.join(prefs['BASEDIR'], 'port_calibration.json') if os.path.exists(cal_path): try: with open(cal_path, 'r') as calf: cal_fns = json.load(calf) prefs['PORT_CALIBRATION'] = cal_fns except json.decoder.JSONDecodeError: warnings.warn(f'calibration file was malformed. Renaming to avoid using in the future') os.rename(cal_path, cal_path + '.bak') elif os.path.exists(cal_raw): # aka raw calibration results exist but no fit has been computed try: luts = compute_calibration(path=cal_raw, do_return=True) with open(cal_path, 'w') as calf: json.dump(luts, calf) prefs['PORT_CALIBRATION'] = luts except json.decoder.JSONDecodeError: warnings.warn(f'processed calibration file was malformed. Renaming to avoid using in the future') os.rename(cal_raw, cal_raw + '.bak') ########################### global _PREFS for k, v in prefs.items(): # globals()[k] = v _PREFS[k] = v # also store as a dictionary so other modules can have one if they want it # globals()['__dict__'] = prefs if using_manager: initialized = globals()['_INITIALIZED'].value = True else: initialized = globals()['_INITIALIZED'] = True
[docs]def add(param, value): """ Add a pref after init Args: param (str): Allcaps parameter name value: Value of the pref """ globals()[param] = value global _PREFS _PREFS[param] = value
# Return the git revision as a string
[docs]def git_version(repo_dir): """ Get the git hash of the current commit. Stolen from `numpy's setup <>`_ and linked by ryanjdillon on `SO <>`_ Args: repo_dir (str): directory of the git repository. Returns: unicode: git commit hash. """ def _minimal_ext_cmd(cmd): # type: (list[str]) -> str # construct minimal environment env = {} for k in ['SYSTEMROOT', 'PATH']: v = os.environ.get(k) if v is not None: env[k] = v # LANGUAGE is used on win32 env['LANGUAGE'] = 'C' env['LANG'] = 'C' env['LC_ALL'] = 'C' out = subprocess.Popen(cmd, stdout = subprocess.PIPE, env=env).communicate()[0] return out out = _minimal_ext_cmd(['git','-C',repo_dir, 'rev-parse', 'HEAD']) GIT_REVISION = out.strip().decode('ascii') return GIT_REVISION
[docs]def compute_calibration(path=None, calibration=None, do_return=False): """ Args: path: calibration: do_return: Returns: """ # FIXME: UGLY HACK - move this function to another module import pandas as pd from scipy.stats import linregress if not calibration: # if we weren't given calibration results, load them if path: open_fn = path else: open_fn = "/usr/autopilot/port_calibration.json" with open(open_fn, 'r') as open_f: calibration = json.load(open_f) luts = {} for port, samples in calibration.items(): sample_df = pd.DataFrame(samples) # TODO: Filter for only most recent timestamps # volumes are saved in mL because of how they are measured, durations are stored in ms # but reward volumes are typically in the uL range, so we make the conversion # by multiplying by 1000 line_fit = linregress((sample_df['vol'] / sample_df['n_clicks']) * 1000., sample_df['dur']) luts[port] = {'intercept': line_fit.intercept, 'slope': line_fit.slope} # write to file, overwriting any previous if do_return: return luts else: # do write lut_fn = os.path.join(globals()['BASEDIR'], 'port_calibration_fit.json') with open(lut_fn, 'w') as lutf: json.dump(luts, lutf)
[docs]def clear(): """ Mostly for use in testing, clear loaded prefs (without deleting prefs.json) (though you will probably overwrite prefs.json if you clear and then set another pref so don't use this except in testing probably) """ global _PREFS global _PREF_MANAGER if using_manager: _PREFS = _PREF_MANAGER.dict() else: _PREFS = {}
#######################3 if using_manager: if not _INITIALIZED.value: init() else: if not _INITIALIZED: init()