auto-trainer-core 2.0.3__tar.gz

auto_trainer_core-2.0.3/PKG-INFO

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+Metadata-Version: 2.1
+Name: auto-trainer-core
+Version: 2.0.3
+Summary: Core objects and implementations for autotrainer
+License: MIT
+Requires-Python: >=3.8
+Requires-Dist: auto-trainer-api==0.9.17
+Requires-Dist: verboselogs<2,>=1.7
+Requires-Dist: coloredlogs<16,>=15
+Requires-Dist: events<1,>=0.5
+Requires-Dist: transitions<1,>=0.9.2
+Requires-Dist: psutil<8,>=7
+Requires-Dist: numpy<2,>=1.23.5
+Requires-Dist: pyhumps<4,>=3.8
+Requires-Dist: pyyaml<7,>=6.0.2
+Requires-Dist: importlib-resources; python_version < "3.10"
+Requires-Dist: importlib-metadata; python_version < "3.10"

auto_trainer_core-2.0.3/README.md

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+# Autotrainer - Core
+
+This is the base module for functions and objects that used across most or all modules and applications.
+
+Major Elements
+* Observable object implementation
+* Common Protocols used to bridge different modules
+* General pub-sub notification hub implementation
+* Event manager for structured application event recording
+* Enhanced multiprocessing shared array behavior
+* General "project" and animal subject data and management
+* Fundamental data analysis operations that may be used ro replay/reprocess data, not just in live capture
+* System configuration reading and persistence
+* Misc utilities
+  * Performance monitoring wrappers
+  * Queue extensions
+
+### Future Work
+The Project class and functionality is largely geared towards the creation of projects, knowing where to save
+data and created those folders and files where necessary.  It should be improved to make it easier to use as 
+a reader for tools that need to be aware of those folders and files, but never create them.  This will be used
+by the management console to read information without needed to burden the acquisition application directly.
+
+System configuration files have been updated to use YAML tags for typing and with a new structure that better
+aligns to the subsystems and their properties.  There is a still a step to separate a) device values that
+are unlikely to change over time (e.g., hardware ports), b) values related to application that can change
+between sessions, but would not be considered "training" variables and c) training variables that users
+are likely to change regularly and in some cases may be changed by hand.

auto_trainer_core-2.0.3/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools >= 61",
+    'setuptools-scm >= 9.2.2, < 10',
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["autotrainer"]
+namespaces = true
+
+[project]
+name = "auto-trainer-core"
+description = "Core objects and implementations for autotrainer"
+license = { text = "MIT" }
+requires-python = ">=3.8"
+dynamic = ["version"]
+
+dependencies = [
+
+    'auto-trainer-api == 0.9.17',
+
+    "verboselogs >= 1.7, < 2",
+    "coloredlogs >= 15, < 16",
+
+    'events >= 0.5, < 1',   # dynamic events callback handling
+    'transitions >= 0.9.2, < 1',  # machine state transition handling
+    'psutil >= 7, < 8',  # for free disk space, notably
+
+    'numpy >= 1.23.5, < 2',
+
+    'pyhumps >= 3.8, < 4',  # snake/camel case converter
+    'pyyaml >= 6.0.2, < 7',
+
+    'importlib-resources; python_version < "3.10"',
+    'importlib-metadata; python_version < "3.10"'
+]
+
+[tool.setuptools_scm]
+root = ".."  # temporary while embedded in autotrainer main repo
+# also strip auto-trainer-core when moved as independent repo
+write_to = "auto-trainer-core/src/autotrainer/core/version.txt"
+git_describe_command = "git describe --tags --dirty --match 'core-v*' --abbrev=8"

auto_trainer_core-2.0.3/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

auto_trainer_core-2.0.3/src/auto_trainer_core.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: auto-trainer-core
+Version: 2.0.3
+Summary: Core objects and implementations for autotrainer
+License: MIT
+Requires-Python: >=3.8
+Requires-Dist: auto-trainer-api==0.9.17
+Requires-Dist: verboselogs<2,>=1.7
+Requires-Dist: coloredlogs<16,>=15
+Requires-Dist: events<1,>=0.5
+Requires-Dist: transitions<1,>=0.9.2
+Requires-Dist: psutil<8,>=7
+Requires-Dist: numpy<2,>=1.23.5
+Requires-Dist: pyhumps<4,>=3.8
+Requires-Dist: pyyaml<7,>=6.0.2
+Requires-Dist: importlib-resources; python_version < "3.10"
+Requires-Dist: importlib-metadata; python_version < "3.10"

auto_trainer_core-2.0.3/src/auto_trainer_core.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+src/auto_trainer_core.egg-info/PKG-INFO
+src/auto_trainer_core.egg-info/SOURCES.txt
+src/auto_trainer_core.egg-info/dependency_links.txt
+src/auto_trainer_core.egg-info/requires.txt
+src/auto_trainer_core.egg-info/top_level.txt
+src/autotrainer/core/__init__.py
+src/autotrainer/core/capture.py
+src/autotrainer/core/diamond_triangle_config.py
+src/autotrainer/core/fixed_array_multiqueue.py
+src/autotrainer/core/fixed_array_queue.py
+src/autotrainer/core/frame_index.py
+src/autotrainer/core/interfaces.py
+src/autotrainer/core/logging.py
+src/autotrainer/core/multiproc.py
+src/autotrainer/core/observable_object.py
+src/autotrainer/core/perf_monitor.py
+src/autotrainer/core/pose_elements.py
+src/autotrainer/core/queue_util.py
+src/autotrainer/core/reach_event.py
+src/autotrainer/core/video_detection.py
+src/autotrainer/core/analysis/__init__.py
+src/autotrainer/core/analysis/alarm_monitor.py
+src/autotrainer/core/analysis/audio_spectrum_data.py
+src/autotrainer/core/analysis/audio_spectrum_monitor.py
+src/autotrainer/core/analysis/auto_tunnel_fan_monitor.py
+src/autotrainer/core/analysis/detector.py
+src/autotrainer/core/analysis/external_doors_monitor.py
+src/autotrainer/core/analysis/global_animal_presence_monitor.py
+src/autotrainer/core/analysis/head_fix_measurement.py
+src/autotrainer/core/analysis/headbar_pressure_monitor.py
+src/autotrainer/core/analysis/load_cell_monitor.py
+src/autotrainer/core/analysis/load_cell_tare_monitor.py
+src/autotrainer/core/analysis/measurement_data.py
+src/autotrainer/core/analysis/pellet_position_monitor.py
+src/autotrainer/core/analysis/sensor_analysis.py
+src/autotrainer/core/analysis/system_fault_monitor.py
+src/autotrainer/core/analysis/system_maintenance_monitor.py
+src/autotrainer/core/animal/__init__.py
+src/autotrainer/core/animal/animal_subject.py
+src/autotrainer/core/configuration/__init__.py
+src/autotrainer/core/configuration/alarm_configuration.py
+src/autotrainer/core/configuration/animal_presence_configuration.py
+src/autotrainer/core/configuration/behavior_configuration.py
+src/autotrainer/core/configuration/camera_configuration.py
+src/autotrainer/core/configuration/external_doors_monitor_configuration.py
+src/autotrainer/core/configuration/hardware_configuration.py
+src/autotrainer/core/configuration/inference_configuration.py
+src/autotrainer/core/configuration/load_cell_config.py
+src/autotrainer/core/configuration/persistence_configuration.py
+src/autotrainer/core/configuration/presence_detection_configuration.py
+src/autotrainer/core/configuration/system_configuration.py
+src/autotrainer/core/configuration/system_fault_config.py
+src/autotrainer/core/configuration/system_maintenance_config.py
+src/autotrainer/core/event/__init__.py
+src/autotrainer/core/event/api_event_kind.py
+src/autotrainer/core/event/api_event_plugin.py
+src/autotrainer/core/event/event_info.py
+src/autotrainer/core/event/event_manager.py
+src/autotrainer/core/event/event_manager_plugin.py
+src/autotrainer/core/event/file_event_plugin.py
+src/autotrainer/core/event/logger_event_plugin.py
+src/autotrainer/core/message/__init__.py
+src/autotrainer/core/message/audio_spectrum_message.py
+src/autotrainer/core/message/measurement_message.py
+src/autotrainer/core/message/message_handler.py
+src/autotrainer/core/message/motor_configuration_message.py
+src/autotrainer/core/message/system_command_kind.py
+src/autotrainer/core/message/system_message_handler.py
+src/autotrainer/core/message/system_status_message.py
+src/autotrainer/core/notification/__init__.py
+src/autotrainer/core/notification/notification_center.py
+src/autotrainer/core/notification/trigger_notification.py
+src/autotrainer/core/project/__init__.py
+src/autotrainer/core/project/project_info.py
+tests/alarm_config_test.py
+tests/animal_config_test.py
+tests/audio_spectrum_monitor_test.py
+tests/event_manager_test.py
+tests/fixed_array_queue_test.py
+tests/frame_index_test.py
+tests/load_cell_monitor_test.py
+tests/load_cell_tare_monitor_test.py
+tests/offset3d_test.py
+tests/pose_elements_test.py
+tests/pressure_threshold_test.py
+tests/project_info_test.py
+tests/system_configuration_test.py
+tests/system_data_args_kwargs_test.py
+tests/fixtures/pressure_threshold_sample.csv
+tests/fixtures/v0_config.yaml
+tests/fixtures/v1_config.yaml
+tests/mocks/__init__.py
+tests/mocks/mock_event_plugin.py

auto_trainer_core-2.0.3/src/auto_trainer_core.egg-info/dependency_links.txt

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+

auto_trainer_core-2.0.3/src/auto_trainer_core.egg-info/requires.txt

@@ -0,0 +1,13 @@
+auto-trainer-api==0.9.17
+verboselogs<2,>=1.7
+coloredlogs<16,>=15
+events<1,>=0.5
+transitions<1,>=0.9.2
+psutil<8,>=7
+numpy<2,>=1.23.5
+pyhumps<4,>=3.8
+pyyaml<7,>=6.0.2
+
+[:python_version < "3.10"]
+importlib-resources
+importlib-metadata

auto_trainer_core-2.0.3/src/auto_trainer_core.egg-info/top_level.txt

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+autotrainer

auto_trainer_core-2.0.3/src/autotrainer/core/__init__.py

@@ -0,0 +1,319 @@
+import dataclasses
+import math
+import time
+from collections import namedtuple
+from typing import Union, List, Tuple, Dict, Any, Iterable, TypeVar, Type, Optional, Callable
+from typing_extensions import Self
+
+import humps
+import yaml
+from typing_extensions import Self
+
+# NB: import order is very important, put the less specific/most general first, then go in order of dependency.
+
+from .logging import get_verbose_logger
+
+#
+
+logger = get_verbose_logger(__name__)
+
+#
+
+def mean_method(data):
+    return sum(data) / len(data)
+
+
+def calculate_std_dev_manual(data, reduce_method=mean_method):
+    n = len(data)
+    if n < 2:
+        raise ValueError("Data must contain at least two values to calculate standard deviation.")
+    res = reduce_method(data)
+    squared_diffs = [(x - res) ** 2 for x in data]
+    variance = sum(squared_diffs) / (n - 1)  # Sample standard deviation
+    std_dev = variance ** 0.5
+    return res, std_dev
+
+#
+
+@dataclasses.dataclass
+class RawValueHolder:
+    value: Any
+
+
+def _no_convert(v):
+    return v
+
+
+class ValueHolderDescriptor:
+
+    def __init__(
+        self,
+        *,
+        convert_to: Callable[[Any], Any] = _no_convert,
+        convert_from: Callable[[Any], Any] = _no_convert,
+    ):
+        self._convert_to = convert_to
+        self._convert_from = convert_from
+
+    def __set_name__(self, owner, name):
+        self.name = name
+        self._priv_name = f"_{name}"
+
+    def __get__(self, instance, owner):
+        if instance is None:
+            return self
+        return self._convert_from(getattr(instance, self._priv_name).value)
+
+    def __set__(self, instance, value):
+        getattr(instance, self._priv_name).value = self._convert_to(value)
+
+#
+
+def transitions_allow_functions(transitions: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """Update the dicts to the functions name"""
+    for trans in transitions:
+        for k in ('trigger', 'before', 'after', 'conditions'):
+            v = trans.get(k)
+            if isinstance(v, (list, tuple)):
+                trans[k] = tuple(
+                    sub.__name__ if callable(sub) else sub
+                    for sub in v
+                )
+            elif callable(v):
+                trans[k] = v.__name__
+    return transitions
+#
+
+Pairs3dOffsetT = Union[List[Tuple[str, str]], Tuple[Tuple[str, str], ...]]
+
+_Offset3DTuple = namedtuple("Offset3DTuple", ('x', 'y', 'z'))
+
+
+def _get_perf_now():
+    # allowed to be patched from test
+    return time.perf_counter()
+
+
+def get_perf_now():
+    return _get_perf_now()
+
+
+class Offset3DTuple(_Offset3DTuple):
+    """Named tuple (x, y, z),
+    allowing construction with "packed" Offset3DTuple((x, y, z)) or "unpacked" Offset3DTuple(x, y, z) coordinates.
+    When "packed": any object having a len() == 3 will be unpacked using python regular:
+        x, y, z = args[0]
+    Otherwise the construction fails (with anything else in args[0] when len(args) == 1)
+    """
+    x: float
+    y: float
+    z: float
+
+    def __new__(cls, *args, **kwargs):
+        if len(args) == 1:
+            arg0 = args[0]
+            if hasattr(arg0, "__len__") and len(arg0) == 3:
+                x, y, z = arg0
+                return super().__new__(cls, x, y, z, **kwargs)  # noqa
+        return super().__new__(cls, *args, **kwargs)  # noqa
+
+    def __repr__(self):
+        # to not get "Offset3DTuple(x, y, z)" but instead only "(x, y, z)"
+        return str(tuple(self))
+
+    __str__ = __repr__
+
+    @staticmethod
+    def get_nan() -> Self:
+        return _nan_offset3d_tuple
+
+    @staticmethod
+    def get_zero() -> Self:
+        return _zero_offset3d_tuple
+
+    def replace(self, x: Optional[float] = None, y: Optional[float] = None, z: Optional[float] = None) -> Self:
+        return self.__class__(
+            self.x if x is None else x,
+            self.y if y is None else y,
+            self.z if z is None else z,
+        )
+
+    def humanize(self, n_digits: int = 2) -> str:
+        x, y, z = self
+        return f"({x:.0{n_digits}f}, {y:.0{n_digits}f}, {z:.0{n_digits}f})"
+
+    def round(self, n: int=2) -> Self:
+        return self.__class__(*(round(v, n) for v in self))
+
+    # tried to use with statistics.mean, but at some point with it there is a sorting applied on the list (of offsets),
+    # and a smaller-than (<) operator check against a start value of 0 .. and we don't handle that with Offset3DTuple.
+    # def as_integer_ratio(self) -> Tuple[Self, Self]:
+    #     # use float(v) to ensure float, and allow use of as_integer_ration, if integer is in any of x/y/z.
+    #     xo, yo, zo = map(lambda v: float(v).as_integer_ratio(), self)
+    #     return self.__class__(xo[0], yo[0], zo[0]), self.__class__(xo[1], yo[1], zo[1])
+
+    def __pow__(self, other, modulo=None) -> Self:
+        if modulo is None:
+            return self.__class__(*(v ** other for v in self))
+        return self.__class__(
+            *(pow(v, other, modulo) for v in self)
+        )
+
+    def __rpow__(self, other, modulo=None) -> Self:
+        if modulo is None:
+            return self.__class__(*(other ** v for v in self))
+        return self.__class__(
+            *(pow(other, v, modulo) for v in self)
+        )
+
+
+    def __add__(self, other) -> Self:
+        if hasattr(other, "__len__") and len(other) == 3:
+            return self.__class__(*(v1 + v2 for v1, v2 in zip(self, other)))
+        return self.__class__(*(v + other for v in self))
+
+    __radd__ = __add__
+
+    def __sub__(self, other) -> Self:
+        if hasattr(other, "__len__") and len(other) == 3:
+            return self.__class__(*(v1 - v2 for v1, v2 in zip(self, other)))
+        return self.__class__(*(v - other for v in self))
+
+    def __rsub__(self, other) -> Self:
+        if hasattr(other, "__len__") and len(other) == 3:
+            return self.__class__(*(v2 - v1 for v1, v2 in zip(self, other)))
+        return self.__class__(*(other - v for v in self))
+
+    def __neg__(self) -> Self:
+        return self.__class__(-self.x, -self.y, -self.z)
+
+    def __mul__(self, other) -> Self:
+        if hasattr(other, "__len__") and len(other) == 3:
+            return self.__class__(*(v1 * v2 for v1, v2 in zip(self, other)))
+        return self.__class__(*(v * other for v in self))
+
+    __rmul__ = __mul__
+
+    def __truediv__(self, other) -> Self:
+        if hasattr(other, "__len__") and len(other) == 3:
+            return self.__class__(*(v1 / v2 for v1, v2 in zip(self, other)))
+        return self.__class__(*(v / other for v in self))
+
+    def __abs__(self) -> Self:
+        return self.__class__(*(abs(v) for v in self))
+
+    @property
+    def distance(self) -> float:
+        return math.sqrt(sum(c**2 for c in self))
+
+
+_nan_offset3d_tuple = Offset3DTuple(math.nan, math.nan, math.nan)
+_zero_offset3d_tuple = Offset3DTuple(0, 0, 0)
+
+#
+
+
+def build_kwargs_apply_mapping(
+    content: Dict[str, Any],
+    mapping: Iterable[Union[str, Tuple[str, str]]],
+    *,
+    skip_remaining: bool = False,
+) -> Dict[str, Any]:
+    kwargs = {}
+    content = dict(content)  # make copy of 1 level given we'll remove/pop from it
+    for cur_map in mapping:
+        if isinstance(cur_map, str):
+            dest = key = cur_map
+        else:
+            assert len(cur_map) == 2
+            dest, key = cur_map
+        if key in content:
+            value = content.pop(key)
+            if dest not in kwargs:  # first one wins
+                kwargs[dest] = value
+    # insert whatever remains in content, unless skipped:
+    if not skip_remaining:
+        kwargs.update(content)
+    return kwargs
+
+#
+
+
+ConfigItemCls = TypeVar("ConfigItemCls")
+
+
+def make_camelize_representer(section_name: str):
+
+    def representer(dumper: yaml.SafeDumper, obj):
+        return dumper.represent_mapping(section_name, {
+            humps.camelize(field.name): getattr(obj, field.name)
+            for field in dataclasses.fields(obj)
+        })
+
+    return representer
+
+
+def make_decamelize_constructor(cls: Type[ConfigItemCls]):
+
+    # required delayed import for now,
+    # not big deal given this function is to be called once only (per config class).
+    from .configuration import SystemConfigurationLoader
+
+    def constructor(loader: SystemConfigurationLoader, node: yaml.nodes.MappingNode) -> ConfigItemCls:
+        content = loader.construct_mapping(node, deep=True)
+        content = humps.decamelize(content)  # decamelize first,
+        # "decamelized" names are here after checked against field names
+        if loader.safe_load:
+            names = [f.name for f in dataclasses.fields(cls)]
+            before_count = len(content)
+            before_s = set(content)
+            content = {
+                k: v
+                for k, v in content.items()
+                if k in names
+            }
+            filtered_count = before_count - len(content)
+            after_s = set(content)
+            if filtered_count != 0:
+                logger.verbose("%s: safe load filtered %s unknown properties/attributes: %s",
+                               cls.__qualname__, filtered_count, sorted(list(before_s - after_s)))
+        return cls(**content)
+
+    return constructor
+
+
+
+# MUST come first (but after above definitions):
+import autotrainer.core.logging
+import autotrainer.core.diamond_triangle_config
+# ..
+
+
+from .observable_object import ObservableObject, ObservableObjectProtocol
+
+from .frame_index import FrameIndexCategory
+
+from .fixed_array_multiqueue import FixedArrayMultiQueue
+from .fixed_array_queue import FixedArrayQueue
+
+from .project import ProjectInfo, ProjectInterval, video_write_ext
+from .animal import AnimalSubject
+
+from .perf_monitor import PerfMonitor
+from .queue_util import clear_queue
+from .notification import NotificationCenter, Notification, TriggerNotification, post_trigger_enable
+from .configuration import HardwareConfiguration, InferenceConfiguration, PersistenceConfiguration
+
+from .message import MotorConfigurations, Motor
+from .message import SystemStatusMessageKind, SystemCommandKind, MeasurementMessageProtocol, AudioSpectrumMessage
+from .configuration import SystemConfiguration, BehaviorConfiguration, CameraConfiguration, CameraId, \
+    SystemConfigurationLoader
+
+from .message import MessageHandler, SystemMessageHandler
+from .analysis import SensorAnalysis, MeasurementData, AudioSpectrumData
+from .analysis import LoadCellMonitor, HeadbarPressureMonitor
+
+from .event.api_event_kind import ApiEventKind
+from .event.event_info import EventInfo
+from .event.api_event_plugin import EventManagerPlugin
+from .event.event_manager import EventManager

auto_trainer_core-2.0.3/src/autotrainer/core/analysis/__init__.py

@@ -0,0 +1,6 @@
+from .audio_spectrum_data import AudioSpectrumData
+from .headbar_pressure_monitor import (HeadbarPressureMonitor, HeadbarPressureConfiguration)
+from .load_cell_monitor import LoadCellMonitor
+from .measurement_data import MeasurementData
+from .alarm_monitor import EmergencyAlarmMonitor
+from .sensor_analysis import SensorAnalysis