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Respir-OS
Respir-OS
Commit 0658772c authored by Víctor Vázquez Rodríguez's avatar Víctor Vázquez Rodríguez
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Merge branch 'devel' into 'master' 

Update build system and dependecy management

See merge request !1
parents 145aaaf0 481e2d6e
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    .gitlab-ci.yml 0 → 100644
    View file @ 0658772c
    image: python:3.7
    before_script:
    - pip install poetry
    - poetry config virtualenvs.create false
    - poetry install
    Publish to PyPI:
    stage: deploy
    only:
    - tags
    script:
    - poetry build
    - poetry publish
    README.md
    View file @ 0658772c
    # respiros-system # Respir-OS
    \ No newline at end of file
    A medical ventilator system for the Raspberry Pi! Detailed information about
    the design, installation and usage can be found on [the
    wiki](https://ohwr.org/project/respir-os/wikis/home).
    api/__main__.py deleted 100644 → 0
    View file @ 145aaaf0
    from gevent.pywsgi import WSGIServer
    from api import create_app
    app = create_app()
    WSGIServer(("", app.config["PORT"]), app).serve_forever()
    controls/__main__.py deleted 100644 → 0
    View file @ 145aaaf0
    from controls import create_app
    app = create_app()
    app.run()
    gui/__main__.py deleted 100644 → 0
    View file @ 145aaaf0
    from gui import create_app
    app = create_app()
    app.run()
    poetry.lock 0 → 100644
    View file @ 0658772c
    This diff is collapsed.
    pyproject.toml 0 → 100644
    View file @ 0658772c
    [tool.poetry]
    name = "respir-os"
    version = "0.1.0"
    description = "Fully-functional ventilator system for the Raspberry Pi."
    authors = [
    "José Sánchez <josesanchez.oncort@gmail.com>",
    "Ismael Martel <ismael.martel@gmail.com>",
    "Carlos García <carlos.garcia@iesppg.net>",
    "Ladislao Martínez <ladislao.m.garcia@gmail.com>",
    "Jaime Lozano <jaimelozano@ugr.es>",
    "Elio Valenzuela <elio@ugr.es>",
    "Abel Cano <abelcano@ugr.es>"
    ]
    maintainers = [
    "Víctor Vázquez <victorvazrod@ugr.es>",
    "Carlos Megías <narg@ugr.es>"
    ]
    license = "LGPL-3.0-or-later"
    repository = "https://ohwr.org/project/respir-os"
    documentation = "https://ohwr.org/project/respir-os/wikis/home"
    readme = "README.md"
    keywords = [
    "Healthcare",
    "Raspberry Pi",
    "Ventilator"
    ]
    classifiers = [
    "Programming Language :: Python :: 3.7",
    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
    "Intended Audience :: Healthcare Industry",
    "Natural Language :: Spanish",
    "Operating System :: Unix"
    ]
    packages = [
    { include = "respir_os" }
    ]
    [tool.poetry.dependencies]
    python = "^3.7"
    Flask = "^2.0.1"
    Flask-SocketIO = "^5.1.0"
    pigpio = "^1.78"
    PySimpleGUI = "^4.45.0"
    matplotlib = "^3.4.2"
    numpy = "^1.21.0"
    gevent = "^21.1.2"
    pyzmq = "^22.1.0"
    [tool.poetry.dev-dependencies]
    black = "^21.6b0"
    [tool.poetry.scripts]
    respir-os = "respir_os.__main__:main"
    [build-system]
    requires = ["poetry-core>=1.0.0"]
    build-backend = "poetry.core.masonry.api"
    requirements-dev.txt deleted 100644 → 0
    View file @ 145aaaf0
    -r requirements.txt
    appdirs==1.4.4
    black==20.8b1
    click==7.1.2
    flake8==3.9.0
    mccabe==0.6.1
    mypy-extensions==0.4.3
    pathspec==0.8.1
    pycodestyle==2.7.0
    pyflakes==2.3.0
    regex==2020.11.13
    toml==0.10.2
    typed-ast==1.4.2
    typing-extensions==3.7.4.3
    requirements.txt deleted 100644 → 0
    View file @ 145aaaf0
    bidict==0.21.2
    click==7.1.2
    cycler==0.10.0
    Flask==1.1.2
    Flask-SocketIO==5.0.1
    gevent==21.1.2
    greenlet==1.0.0
    itsdangerous==1.1.0
    Jinja2==2.11.3
    kiwisolver==1.3.1
    MarkupSafe==1.1.1
    matplotlib==3.3.4
    numpy==1.20.1
    pigpio==1.78
    Pillow==8.1.2
    pyparsing==2.4.7
    PySimpleGUI==4.36.0
    python-dateutil==2.8.1
    python-engineio==4.0.1
    python-socketio==5.1.0
    pyzmq==22.0.3
    six==1.15.0
    Werkzeug==1.0.1
    zope.event==4.5.0
    zope.interface==5.2.0
    respir_os/__main__.py 0 → 100644
    View file @ 0658772c
    import os
    from multiprocessing import Process
    import respir_os.api as api
    import respir_os.controls as controls
    import respir_os.gui as gui
    def main():
    os.environ["ENV"] = "development"
    procs = [
    Process(target=api.run),
    Process(target=controls.run),
    Process(target=gui.run),
    ]
    try:
    for p in procs:
    p.start()
    except KeyboardInterrupt:
    for p in procs:
    p.kill()
    if __name__ == "__main__":
    main()
    api/__init__.py → respir_os/api/__init__.py
    View file @ 0658772c
    ...@@ -2,10 +2,10 @@ import logging ...@@ -2,10 +2,10 @@ import logging
    import os import os
    from flask import Flask from flask import Flask
    from gevent.pywsgi import WSGIServer
    from api.config import Config, DevelopmentConfig from respir_os.api.config import Config, DevelopmentConfig
    from api.ipc import ipc from respir_os.api.ipc import ipc
    from api.sockets import socketio from respir_os.api.sockets import socketio
    def create_app() -> Flask: def create_app() -> Flask:
    ...@@ -28,11 +28,16 @@ def create_app() -> Flask: ...@@ -28,11 +28,16 @@ def create_app() -> Flask:
    logging_level = logging.INFO logging_level = logging.INFO
    else: else:
    logging_level = logging.WARNING logging_level = logging.WARNING
    logging.basicConfig( logging.basicConfig(filename="logs/api.log", filemode="w", level=logging_level)
    filename="logs/api.log", filemode="w", level=logging_level
    )
    socketio.init_app(app) socketio.init_app(app)
    ipc.init_app(app) ipc.init_app(app)
    return app return app
    def run():
    """Run the app."""
    app = create_app()
    WSGIServer(("", app.config["PORT"]), app).serve_forever()
    api/config.py → respir_os/api/config.py
    View file @ 0658772c
    from common.config import BaseConfig from respir_os.common.config import BaseConfig
    class Config(BaseConfig): class Config(BaseConfig):
    ......
    api/ipc.py → respir_os/api/ipc.py
    View file @ 0658772c
    import logging import logging
    import gevent import gevent
    from common.ipc import IPCBuilder, Topic from respir_os.common.ipc import IPCBuilder, Topic
    class IPCDirector: class IPCDirector:
    ...@@ -27,9 +27,7 @@ class IPCDirector: ...@@ -27,9 +27,7 @@ class IPCDirector:
    app.config["ZMQ_SYNC_API_ADDR"], app.config["ZMQ_SYNC_API_ADDR"],
    ) )
    app.ipc = self.__builder.manager app.ipc = self.__builder.manager
    app.extensions["socketio"].start_background_task( app.extensions["socketio"].start_background_task(self.__ipc_watchdog, app)
    self.__ipc_watchdog, app
    )
    def __ipc_watchdog(self, app): def __ipc_watchdog(self, app):
    while True: while True:
    ......
    common/ipc.py → respir_os/common/ipc.py
    View file @ 0658772c
    ...@@ -30,9 +30,7 @@ class IPCManager: ...@@ -30,9 +30,7 @@ class IPCManager:
    self.poller = None self.poller = None
    def send(self, topic: Topic, body: Dict): def send(self, topic: Topic, body: Dict):
    self.pub.send_multipart( self.pub.send_multipart([topic.name.encode(), json.dumps(body).encode()])
    [topic.name.encode(), json.dumps(body).encode()]
    )
    def recv(self, block=True) -> Tuple[Topic, Dict]: def recv(self, block=True) -> Tuple[Topic, Dict]:
    if not self.subs: if not self.subs:
    ......
    controls/__init__.py → respir_os/controls/__init__.py
    View file @ 0658772c
    import logging import logging
    import os import os
    from controls.app import ControlApplication from respir_os.controls.app import ControlApplication
    from controls.config import Config, DevelopmentConfig, TestingConfig from respir_os.controls.config import Config, DevelopmentConfig, TestingConfig
    from controls.context import ctx from respir_os.controls.context import ctx
    from controls.ipc import ipc from respir_os.controls.ipc import ipc
    from controls.pcb.controller import pcb from respir_os.controls.pcb.controller import pcb
    from controls.states.director import sd from respir_os.controls.states.director import sd
    def create_app() -> ControlApplication: def create_app() -> ControlApplication:
    ...@@ -31,9 +31,7 @@ def create_app() -> ControlApplication: ...@@ -31,9 +31,7 @@ def create_app() -> ControlApplication:
    logging_level = logging.INFO logging_level = logging.INFO
    else: else:
    logging_level = logging.WARNING logging_level = logging.WARNING
    logging.basicConfig( logging.basicConfig(filename="logs/controls.log", filemode="w", level=logging_level)
    filename="logs/controls.log", filemode="w", level=logging_level
    )
    ctx.init_app(app) ctx.init_app(app)
    pcb.init_app(app) pcb.init_app(app)
    ...@@ -41,3 +39,10 @@ def create_app() -> ControlApplication: ...@@ -41,3 +39,10 @@ def create_app() -> ControlApplication:
    ipc.init_app(app) ipc.init_app(app)
    return app return app
    def run():
    """Run the app."""
    app = create_app()
    app.run()
    controls/config.py → respir_os/controls/config.py
    View file @ 0658772c
    from common.config import BaseConfig from respir_os.common.config import BaseConfig
    class Config(BaseConfig): class Config(BaseConfig):
    ......
    controls/context.py → respir_os/controls/context.py
    View file @ 0658772c
    ...@@ -2,7 +2,7 @@ from dataclasses import dataclass ...@@ -2,7 +2,7 @@ from dataclasses import dataclass
    from datetime import datetime from datetime import datetime
    from typing import Set from typing import Set
    from common.alarms import Alarm, Type, Criticality from respir_os.common.alarms import Alarm, Criticality, Type
    @dataclass @dataclass
    ...@@ -54,9 +54,7 @@ class Context: ...@@ -54,9 +54,7 @@ class Context:
    self.freq_max = app.config["ALARM_FREQ_MAX"] self.freq_max = app.config["ALARM_FREQ_MAX"]
    timestamp = datetime.now() timestamp = datetime.now()
    self.alarms = set( self.alarms = set([Alarm(t, Criticality.NONE, timestamp) for t in Type])
    [Alarm(t, Criticality.NONE, timestamp) for t in Type]
    )
    app.ctx = self app.ctx = self
    ......
    controls/ipc.py → respir_os/controls/ipc.py
    View file @ 0658772c
    from common.ipc import IPCBuilder, Topic from respir_os.common.ipc import IPCBuilder, Topic
    class IPCDirector: class IPCDirector:
    ......
    controls/pcb/analog.py → respir_os/controls/pcb/analog.py
    View file @ 0658772c
    ...@@ -14,9 +14,7 @@ class AnalogConverter: ...@@ -14,9 +14,7 @@ class AnalogConverter:
    An MCP3008 analog to digital converter. An MCP3008 analog to digital converter.
    """ """
    def __init__( def __init__(self, pi: pigpio.pi, channel: int, baud_rate: int, voltage: float):
    self, pi: pigpio.pi, channel: int, baud_rate: int, voltage: float
    ):
    """ """
    Instantiate a new ADC connected to the Pi. Instantiate a new ADC connected to the Pi.
    ......
    controls/pcb/servo.py → respir_os/controls/pcb/servo.py
    View file @ 0658772c
    ...@@ -9,9 +9,7 @@ class Servo: ...@@ -9,9 +9,7 @@ class Servo:
    A continuous servo that moves between 0 and 180 degrees. A continuous servo that moves between 0 and 180 degrees.
    """ """
    def __init__( def __init__(self, pi: pigpio.pi, gpio_pin: int, min_width: int, max_width: int):
    self, pi: pigpio.pi, gpio_pin: int, min_width: int, max_width: int
    ):
    """ """
    Instantiate a new servo connected to the Pi on the given GPIO pin. Instantiate a new servo connected to the Pi on the given GPIO pin.
    ...@@ -42,7 +40,5 @@ class Servo: ...@@ -42,7 +40,5 @@ class Servo:
    if angle < 0 or angle > 180: if angle < 0 or angle > 180:
    raise ValueError("The angle must be between 0 and 180 degrees.") raise ValueError("The angle must be between 0 and 180 degrees.")
    width = (angle / 180) * ( width = (angle / 180) * (self.max_width - self.min_width) + self.min_width
    self.max_width - self.min_width
    ) + self.min_width
    self.pi.set_servo_pulsewidth(self.gpio_pin, width) self.pi.set_servo_pulsewidth(self.gpio_pin, width)
    controls/states/director.py → respir_os/controls/states/director.py
    View file @ 0658772c
    import controls.states as states import respir_os.controls.states as states
    class StateDirector: class StateDirector:
    ......
    controls/states/operation.py → respir_os/controls/states/operation.py
    View file @ 0658772c
    from datetime import datetime
    import logging import logging
    import time import time
    from datetime import datetime
    from typing import Dict from typing import Dict
    import numpy as np import numpy as np
    import zmq import zmq
    from common.alarms import Alarm, Criticality, Type from respir_os.common.alarms import Alarm, Criticality, Type
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from controls.context import Context from respir_os.controls.context import Context
    from .state import State from .state import State
    ...@@ -137,17 +137,11 @@ class OperationState(State): ...@@ -137,17 +137,11 @@ class OperationState(State):
    # operation # operation
    if not self.operation: if not self.operation:
    if ( if (
    not insp_exp not insp_exp and time.time() >= self.time_saved + self.insp_duration
    and time.time() >= self.time_saved + self.insp_duration ) or (insp_exp and time.time() >= self.time_saved + self.esp_duration):
    ) or (
    insp_exp
    and time.time() >= self.time_saved + self.esp_duration
    ):
    insp_exp = not insp_exp insp_exp = not insp_exp
    if ( if insp_exp: # Start espiration, save inspiration parameters
    insp_exp
    ): # Start espiration, save inspiration parameters
    self.__start_espiration() self.__start_espiration()
    logging.info("Espiration Controlled") logging.info("Espiration Controlled")
    ...@@ -158,24 +152,15 @@ class OperationState(State): ...@@ -158,24 +152,15 @@ class OperationState(State):
    # Assisted Mode Operation: I, E transition. Triggered and airflow # Assisted Mode Operation: I, E transition. Triggered and airflow
    # mode operation # mode operation
    else: else:
    if ( if insp_exp: # Espiration. Detect trigger to change to inspiration.
    insp_exp if time.time() > self.time_saved + self.esp_duration * 1.0 / 3.0:
    ): # Espiration. Detect trigger to change to inspiration.
    if (
    time.time()
    > self.time_saved + self.esp_duration * 1.0 / 3.0
    ):
    if ( if (
    not self.airflow_trigger not self.airflow_trigger
    or self.airflow_trigger or self.airflow_trigger <= self.airflow_pressure_filtered
    <= self.airflow_pressure_filtered
    ): ):
    self.airflow_trigger = ( self.airflow_trigger = self.airflow_pressure_filtered
    self.airflow_pressure_filtered
    )
    elif ( elif (
    self.airflow_trigger self.airflow_trigger - self.airflow_pressure_filtered
    - self.airflow_pressure_filtered
    >= self.app.ctx.trigger >= self.app.ctx.trigger
    and self.airflow_pressure_filtered < 0 and self.airflow_pressure_filtered < 0
    ): ):
    ...@@ -199,9 +184,7 @@ class OperationState(State): ...@@ -199,9 +184,7 @@ class OperationState(State):
    ): ):
    # Start espiration, save inspiration parameters # Start espiration, save inspiration parameters
    logging.info("Airflow max: %f", self.airflow_max) logging.info("Airflow max: %f", self.airflow_max)
    logging.info( logging.info("Airflow: %f", self.airflow_pressure_filtered)
    "Airflow: %f", self.airflow_pressure_filtered
    )
    insp_exp = not insp_exp insp_exp = not insp_exp
    self.__start_espiration() self.__start_espiration()
    logging.info("Espiration Assisted") logging.info("Espiration Assisted")
    ...@@ -210,21 +193,17 @@ class OperationState(State): ...@@ -210,21 +193,17 @@ class OperationState(State):
    if insp_exp: # Espiration if insp_exp: # Espiration
    self.epap_read = ( self.epap_read = (
    (MEAN_IEPAP_LENGTH - 1) / MEAN_IEPAP_LENGTH (MEAN_IEPAP_LENGTH - 1) / MEAN_IEPAP_LENGTH
    ) * self.epap_read + ( ) * self.epap_read + (1 / MEAN_IEPAP_LENGTH) * self.gauge_pressure
    1 / MEAN_IEPAP_LENGTH
    ) * self.gauge_pressure
    self.app.pcb.servo.set_angle(self.epap_angle) self.app.pcb.servo.set_angle(self.epap_angle)
    # Check operation mode change # Check operation mode change
    if ( if (
    not self.operation not self.operation
    and time.time() and time.time() >= self.time_saved + self.esp_duration * 1.0 / 3.0
    >= self.time_saved + self.esp_duration * 1.0 / 3.0
    ): ):
    if ( if (
    not self.airflow_trigger not self.airflow_trigger
    or self.airflow_trigger or self.airflow_trigger <= self.airflow_pressure_filtered
    <= self.airflow_pressure_filtered
    ): ):
    self.airflow_trigger = self.airflow_pressure_filtered self.airflow_trigger = self.airflow_pressure_filtered
    elif ( elif (
    ...@@ -234,18 +213,14 @@ class OperationState(State): ...@@ -234,18 +213,14 @@ class OperationState(State):
    ): ):
    logging.info( logging.info(
    "Trigger difference %f", "Trigger difference %f",
    self.airflow_trigger self.airflow_trigger - self.airflow_pressure_filtered,
    - self.airflow_pressure_filtered,
    ) )
    self.operation = True self.operation = True
    insp_exp = not insp_exp insp_exp = not insp_exp
    self.__start_inspiration() self.__start_inspiration()
    logging.info("Inspiration Assisted") logging.info("Inspiration Assisted")
    elif ( elif self.operation and time.time() >= self.time_saved + APNEA_TIME:
    self.operation
    and time.time() >= self.time_saved + APNEA_TIME
    ):
    self.operation = False self.operation = False
    insp_exp = not insp_exp insp_exp = not insp_exp
    self.__start_inspiration() self.__start_inspiration()
    ...@@ -255,9 +230,7 @@ class OperationState(State): ...@@ -255,9 +230,7 @@ class OperationState(State):
    else: # Inspiration else: # Inspiration
    self.ipap_read = ( self.ipap_read = (
    (MEAN_IEPAP_LENGTH - 1) / MEAN_IEPAP_LENGTH (MEAN_IEPAP_LENGTH - 1) / MEAN_IEPAP_LENGTH
    ) * self.ipap_read + ( ) * self.ipap_read + (1 / MEAN_IEPAP_LENGTH) * self.gauge_pressure
    1 / MEAN_IEPAP_LENGTH
    ) * self.gauge_pressure
    self.app.pcb.servo.set_angle(self.ipap_angle) self.app.pcb.servo.set_angle(self.ipap_angle)
    ...@@ -330,9 +303,7 @@ class OperationState(State): ...@@ -330,9 +303,7 @@ class OperationState(State):
    """Obtain respiration frequency and send cycle info.""" """Obtain respiration frequency and send cycle info."""
    if self.mode: if self.mode:
    self.freq_read = 60 / ( self.freq_read = 60 / (self.insp_duration_read + self.esp_duration_read)
    self.insp_duration_read + self.esp_duration_read
    )
    else: else:
    self.freq_read = 0 self.freq_read = 0
    ...@@ -357,9 +328,7 @@ class OperationState(State): ...@@ -357,9 +328,7 @@ class OperationState(State):
    if self.app.ctx.ipap != self.ipap_old or not self.mode: if self.app.ctx.ipap != self.ipap_old or not self.mode:
    if not self.iepap_index[int(self.app.ctx.ipap - 1)]: if not self.iepap_index[int(self.app.ctx.ipap - 1)]:
    self.ipap_angle = ( self.ipap_angle = 20.009 * np.log(float(self.app.ctx.ipap)) + 37.997
    20.009 * np.log(float(self.app.ctx.ipap)) + 37.997
    )
    else: else:
    self.ipap_angle = self.iepap_table[int(self.app.ctx.ipap - 1)] self.ipap_angle = self.iepap_table[int(self.app.ctx.ipap - 1)]
    self.ipap_old = self.app.ctx.ipap self.ipap_old = self.app.ctx.ipap
    ...@@ -379,9 +348,7 @@ class OperationState(State): ...@@ -379,9 +348,7 @@ class OperationState(State):
    if self.app.ctx.epap != self.epap_old or not self.mode: if self.app.ctx.epap != self.epap_old or not self.mode:
    if not self.iepap_index[int(self.app.ctx.epap - 1)]: if not self.iepap_index[int(self.app.ctx.epap - 1)]:
    self.epap_angle = ( self.epap_angle = 20.009 * np.log(float(self.app.ctx.epap)) + 37.997
    20.009 * np.log(float(self.app.ctx.epap)) + 37.997
    )
    else: else:
    self.epap_angle = self.iepap_table[int(self.app.ctx.epap - 1)] self.epap_angle = self.iepap_table[int(self.app.ctx.epap - 1)]
    self.epap_old = self.app.ctx.epap self.epap_old = self.app.ctx.epap
    ......
    controls/states/self_check.py → respir_os/controls/states/self_check.py
    View file @ 0658772c
    ...@@ -2,7 +2,7 @@ import logging ...@@ -2,7 +2,7 @@ import logging
    import time import time
    from typing import Tuple from typing import Tuple
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from .failure import FailureState from .failure import FailureState
    from .stand_by import StandByState from .stand_by import StandByState
    ...@@ -31,19 +31,13 @@ class SelfCheckState(State): ...@@ -31,19 +31,13 @@ class SelfCheckState(State):
    # TODO: Call the actual functions instead of using static values # TODO: Call the actual functions instead of using static values
    dht_box_ok = True dht_box_ok = True
    logging.info( logging.info("Box DHT sensor status: %s", "OK" if dht_box_ok else "FAIL")
    "Box DHT sensor status: %s", "OK" if dht_box_ok else "FAIL"
    )
    dht_air_ok = True dht_air_ok = True
    logging.info( logging.info("Air DHT sensor status: %s", "OK" if dht_air_ok else "FAIL")
    "Air DHT sensor status: %s", "OK" if dht_air_ok else "FAIL"
    )
    gauge_ok, airflow_ok, servo_ok = (True, True, True) gauge_ok, airflow_ok, servo_ok = (True, True, True)
    logging.info( logging.info("Gauge pressure sensor status: %s", "OK" if dht_air_ok else "FAIL")
    "Gauge pressure sensor status: %s", "OK" if dht_air_ok else "FAIL"
    )
    logging.info( logging.info(
    "Airflow pressure sensor status: %s", "Airflow pressure sensor status: %s",
    "OK" if dht_air_ok else "FAIL", "OK" if dht_air_ok else "FAIL",
    ...@@ -51,9 +45,7 @@ class SelfCheckState(State): ...@@ -51,9 +45,7 @@ class SelfCheckState(State):
    logging.info("Servo status: %s", "OK" if dht_air_ok else "FAIL") logging.info("Servo status: %s", "OK" if dht_air_ok else "FAIL")
    oxygen_ok = True oxygen_ok = True
    logging.info( logging.info("Oxygen sensor status: %s", "OK" if dht_air_ok else "FAIL")
    "Oxygen sensor status: %s", "OK" if dht_air_ok else "FAIL"
    )
    atm_ok = True atm_ok = True
    logging.info( logging.info(
    ...@@ -101,10 +93,7 @@ class SelfCheckState(State): ...@@ -101,10 +93,7 @@ class SelfCheckState(State):
    self.app.pcb.dht_box.trigger() self.app.pcb.dht_box.trigger()
    tmp = self.app.pcb.dht_box.temperature() tmp = self.app.pcb.dht_box.temperature()
    hum = self.app.pcb.dht_box.humidity() hum = self.app.pcb.dht_box.humidity()
    if ( if BOX_TMP_MIN <= tmp <= BOX_TMP_MAX or BOX_HUM_MIN <= hum <= BOX_HUM_MAX:
    BOX_TMP_MIN <= tmp <= BOX_TMP_MAX
    or BOX_HUM_MIN <= hum <= BOX_HUM_MAX
    ):
    return True return True
    time.sleep(2) time.sleep(2)
    ...@@ -145,16 +134,11 @@ class SelfCheckState(State): ...@@ -145,16 +134,11 @@ class SelfCheckState(State):
    gauge_pressure = self.app.pcb.gauge_ps.read() gauge_pressure = self.app.pcb.gauge_ps.read()
    airflow_pressure = self.app.pcb.airflow_ps.read() airflow_pressure = self.app.pcb.airflow_ps.read()
    if ( if angle == 0 and GAUGE_MIN * 0.95 < gauge_pressure < GAUGE_MIN * 1.05:
    angle == 0
    and GAUGE_MIN * 0.95 < gauge_pressure < GAUGE_MIN * 1.05
    ):
    flag_gauge_0_ok = True flag_gauge_0_ok = True
    if ( if (
    angle == 0 angle == 0
    and AIRFLOW_MAX * 0.9 and AIRFLOW_MAX * 0.9 < airflow_pressure < AIRFLOW_MIN * 1.05
    < airflow_pressure
    < AIRFLOW_MIN * 1.05
    ): ):
    flag_flow_0_ok = True flag_flow_0_ok = True
    ...@@ -165,9 +149,7 @@ class SelfCheckState(State): ...@@ -165,9 +149,7 @@ class SelfCheckState(State):
    flag_gauge_180_ok = True flag_gauge_180_ok = True
    if ( if (
    angle == 180 angle == 180
    and AIRFLOW_MAX * 0.95 and AIRFLOW_MAX * 0.95 < airflow_pressure < AIRFLOW_MIN * 1.05
    < airflow_pressure
    < AIRFLOW_MIN * 1.05
    ): ):
    flag_flow_180_ok = True flag_flow_180_ok = True
    ......
    controls/states/stand_by.py → respir_os/controls/states/stand_by.py
    View file @ 0658772c
    import logging import logging
    import time import time
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from .operation import OperationState from .operation import OperationState
    from .state import State from .state import State
    ...@@ -64,9 +64,7 @@ class StandByState(State): ...@@ -64,9 +64,7 @@ class StandByState(State):
    time.sleep(0.0001) time.sleep(0.0001)
    airflow_voltage_offset = self.__calculate_voltage_airflow( airflow_voltage_offset = self.__calculate_voltage_airflow(airflow_offset)
    airflow_offset
    )
    gauge_voltage_offset = self.__calculate_voltage_gauge(gauge_offset) gauge_voltage_offset = self.__calculate_voltage_gauge(gauge_offset)
    self.app.pcb.airflow_ps.func = lambda v: ( self.app.pcb.airflow_ps.func = lambda v: (
    ...@@ -95,9 +93,7 @@ class StandByState(State): ...@@ -95,9 +93,7 @@ class StandByState(State):
    def __calculate_voltage_airflow(self, airflow_offset): def __calculate_voltage_airflow(self, airflow_offset):
    return ( return (
    -172.15 -172.15 + (172.15 ** 2 - 4 * (-19.269) * (-276.2 - airflow_offset)) ** (0.5)
    + (172.15 ** 2 - 4 * (-19.269) * (-276.2 - airflow_offset))
    ** (0.5)
    ) / (2 * (-19.269)) ) / (2 * (-19.269))
    def __calculate_voltage_gauge(self, gauge_offset): def __calculate_voltage_gauge(self, gauge_offset):
    ......
    gui/__init__.py → respir_os/gui/__init__.py
    View file @ 0658772c
    import logging import logging
    import os import os
    from gui.app import GUIApplication from respir_os.gui.app import GUIApplication
    from gui.config import Config, DevelopmentConfig from respir_os.gui.config import Config, DevelopmentConfig
    from gui.context import ctx from respir_os.gui.context import ctx
    from gui.ipc import ipc from respir_os.gui.ipc import ipc
    from gui.views.director import vd from respir_os.gui.views.director import vd
    def create_app() -> GUIApplication: def create_app() -> GUIApplication:
    ...@@ -28,12 +28,17 @@ def create_app() -> GUIApplication: ...@@ -28,12 +28,17 @@ def create_app() -> GUIApplication:
    logging_level = logging.INFO logging_level = logging.INFO
    else: else:
    logging_level = logging.WARNING logging_level = logging.WARNING
    logging.basicConfig( logging.basicConfig(filename="logs/gui.log", filemode="w", level=logging_level)
    filename="logs/gui.log", filemode="w", level=logging_level
    )
    ctx.init_app(app) ctx.init_app(app)
    vd.init_app(app) vd.init_app(app)
    ipc.init_app(app) ipc.init_app(app)
    return app return app
    def run():
    """Run the app."""
    app = create_app()
    app.run()
    gui/config.py → respir_os/gui/config.py
    View file @ 0658772c
    from common.config import BaseConfig from respir_os.common.config import BaseConfig
    class Config(BaseConfig): class Config(BaseConfig):
    ......
    gui/context.py → respir_os/gui/context.py
    View file @ 0658772c
    from dataclasses import dataclass from dataclasses import dataclass
    from typing import List from typing import List
    from common.alarms import Alarm from respir_os.common.alarms import Alarm
    @dataclass @dataclass
    ......
    gui/ipc.py → respir_os/gui/ipc.py
    View file @ 0658772c
    import threading import threading
    from enum import Enum, auto from enum import Enum, auto
    from common.ipc import IPCBuilder, Topic from respir_os.common.ipc import IPCBuilder, Topic
    class ZMQEvent(Enum): class ZMQEvent(Enum):
    ...@@ -43,9 +43,7 @@ class IPCDirector: ...@@ -43,9 +43,7 @@ class IPCDirector:
    ], ],
    ) )
    app.ipc = self.__builder.manager app.ipc = self.__builder.manager
    threading.Thread( threading.Thread(target=self.__ipc_watchdog, args=[app], daemon=True).start()
    target=self.__ipc_watchdog, args=[app], daemon=True
    ).start()
    def __ipc_watchdog(self, app): def __ipc_watchdog(self, app):
    while True: while True:
    ......
    gui/views/director.py → respir_os/gui/views/director.py
    View file @ 0658772c
    import gui.views as views import respir_os.gui.views as views
    class ViewDirector: class ViewDirector:
    ......
    gui/views/loading.py → respir_os/gui/views/loading.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from gui.component import Component from respir_os.gui.component import Component
    from gui.ipc import ZMQEvent from respir_os.gui.ipc import ZMQEvent
    from gui.views.parameters import ParametersView from respir_os.gui.views.parameters import ParametersView
    class LoadingView(Component): class LoadingView(Component):
    ...@@ -24,9 +24,7 @@ class LoadingView(Component): ...@@ -24,9 +24,7 @@ class LoadingView(Component):
    self.expander_top = sg.Text() self.expander_top = sg.Text()
    self.expander_bottom = sg.Text() self.expander_bottom = sg.Text()
    self.layout( self.layout([[self.expander_top], [self.loading_label], [self.expander_bottom]])
    [[self.expander_top], [self.loading_label], [self.expander_bottom]]
    )
    def handle_event(self, event: str, values: Dict): def handle_event(self, event: str, values: Dict):
    if event == ZMQEvent.CHECK.name: if event == ZMQEvent.CHECK.name:
    ...@@ -36,7 +34,5 @@ class LoadingView(Component): ...@@ -36,7 +34,5 @@ class LoadingView(Component):
    self.expand(expand_x=True, expand_y=True) self.expand(expand_x=True, expand_y=True)
    self.expander_top.expand(expand_x=True, expand_y=True) self.expander_top.expand(expand_x=True, expand_y=True)
    self.expander_bottom.expand(expand_x=True, expand_y=True) self.expander_bottom.expand(expand_x=True, expand_y=True)
    self.loading_label.expand( self.loading_label.expand(expand_x=True, expand_y=True, expand_row=False)
    expand_x=True, expand_y=True, expand_row=False
    )
    super().show() super().show()
    gui/views/operation.py → respir_os/gui/views/operation.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from gui.component import Component from respir_os.gui.component import Component
    from gui.widgets.control import ControlPane from respir_os.gui.widgets.control import ControlPane
    from gui.widgets.monitor import MonitorBar from respir_os.gui.widgets.monitor import MonitorBar
    from gui.widgets.plots import PlotCanvas from respir_os.gui.widgets.plots import PlotCanvas
    class OperationView(Component): class OperationView(Component):
    ......
    gui/views/parameters.py → respir_os/gui/views/parameters.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from gui.component import Component from respir_os.gui.component import Component
    from gui.views.operation import OperationView from respir_os.gui.views.operation import OperationView
    from gui.widgets.sliders import IESlider, NumericSlider from respir_os.gui.widgets.sliders import IESlider, NumericSlider
    class ParametersView(Component): class ParametersView(Component):
    """Parameter selection for operation start.""" """Parameter selection for operation start."""
    def __init__(self, app): def __init__(self, app):
    super().__init__( super().__init__(app, pad=(373, 0), visible=False, key="ParametersView")
    app, pad=(373, 0), visible=False, key="ParametersView"
    )
    # Sliders # Sliders
    self.ipap = NumericSlider( self.ipap = NumericSlider(
    ......
    gui/widgets/control/pane.py → respir_os/gui/widgets/control/pane.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from gui.component import Component from respir_os.gui.component import Component
    from gui.ipc import ZMQEvent from respir_os.gui.ipc import ZMQEvent
    from .tabs import AlarmsTab, HistoryTab, ParametersTab from .tabs import AlarmsTab, HistoryTab, ParametersTab
    ......
    gui/widgets/control/tabs/alarms.py → respir_os/gui/widgets/control/tabs/alarms.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from gui.widgets.sliders import NumericSlider from respir_os.gui.widgets.sliders import NumericSlider
    from .tab import ControlTab from .tab import ControlTab
    ......
    gui/widgets/control/tabs/history.py → respir_os/gui/widgets/control/tabs/history.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.alarms import Alarm, Criticality, Type from respir_os.common.alarms import Alarm, Criticality, Type
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from gui.ipc import ZMQEvent from respir_os.gui.ipc import ZMQEvent
    from .tab import ControlTab from .tab import ControlTab
    ...@@ -104,9 +104,7 @@ class HistoryTab(ControlTab): ...@@ -104,9 +104,7 @@ class HistoryTab(ControlTab):
    ) )
    ) )
    self.layout( self.layout([[self.silence_btn]] + [[card] for card in self.alarm_cards])
    [[self.silence_btn]] + [[card] for card in self.alarm_cards]
    )
    def handle_event(self, event: str, values: Dict): def handle_event(self, event: str, values: Dict):
    if event == self.silence_btn.Key: if event == self.silence_btn.Key:
    ......
    gui/widgets/control/tabs/parameters.py → respir_os/gui/widgets/control/tabs/parameters.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.ipc import Topic from respir_os.common.ipc import Topic
    from gui.widgets.sliders import IESlider, NumericSlider from respir_os.gui.widgets.sliders import IESlider, NumericSlider
    from .tab import ControlTab from .tab import ControlTab
    ...@@ -134,18 +134,14 @@ class ParametersTab(ControlTab): ...@@ -134,18 +134,14 @@ class ParametersTab(ControlTab):
    if self.app.ctx.mode.upper() == "VCP": if self.app.ctx.mode.upper() == "VCP":
    self.app.ctx.ipap = self.ipap_vps.value = self.ipap_vcp.value self.app.ctx.ipap = self.ipap_vps.value = self.ipap_vcp.value
    self.app.ctx.epap = self.epap_vps.value = self.epap_vcp.value self.app.ctx.epap = self.epap_vps.value = self.epap_vcp.value
    self.app.ctx.trigger = ( self.app.ctx.trigger = self.trigger_vps.value = self.trigger_vcp.value
    self.trigger_vps.value
    ) = self.trigger_vcp.value
    self.app.ctx.freq = self.freq_vcp.value self.app.ctx.freq = self.freq_vcp.value
    self.app.ctx.inhale = self.ie_vcp.value[0] self.app.ctx.inhale = self.ie_vcp.value[0]
    self.app.ctx.exhale = self.ie_vcp.value[1] self.app.ctx.exhale = self.ie_vcp.value[1]
    else: else:
    self.app.ctx.ipap = self.ipap_vcp.value = self.ipap_vps.value self.app.ctx.ipap = self.ipap_vcp.value = self.ipap_vps.value
    self.app.ctx.epap = self.epap_vcp.value = self.epap_vps.value self.app.ctx.epap = self.epap_vcp.value = self.epap_vps.value
    self.app.ctx.trigger = ( self.app.ctx.trigger = self.trigger_vcp.value = self.trigger_vps.value
    self.trigger_vcp.value
    ) = self.trigger_vps.value
    if self.app.ctx.ipap <= self.app.ctx.epap and event in { if self.app.ctx.ipap <= self.app.ctx.epap and event in {
    self.ipap_vcp.slider.Key, self.ipap_vcp.slider.Key,
    ......
    gui/widgets/control/tabs/tab.py → respir_os/gui/widgets/control/tabs/tab.py
    View file @ 0658772c
    from abc import ABCMeta, abstractmethod from abc import ABCMeta, abstractmethod
    from gui.component import Component from respir_os.gui.component import Component
    class ControlTab(Component, metaclass=ABCMeta): class ControlTab(Component, metaclass=ABCMeta):
    ......
    gui/widgets/monitor.py → respir_os/gui/widgets/monitor.py
    View file @ 0658772c
    from typing import Dict from typing import Dict
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.alarms import Alarm, Criticality, Type from respir_os.common.alarms import Alarm, Criticality, Type
    from gui.component import Component from respir_os.gui.component import Component
    from gui.ipc import ZMQEvent from respir_os.gui.ipc import ZMQEvent
    class DisplayUnit(sg.Column): class DisplayUnit(sg.Column):
    ...@@ -18,9 +18,7 @@ class DisplayUnit(sg.Column): ...@@ -18,9 +18,7 @@ class DisplayUnit(sg.Column):
    self.__value = 0.0 self.__value = 0.0
    self.__metric = metric self.__metric = metric
    self.title_label = sg.Text( self.title_label = sg.Text(f"{title}:", font=(font_family, font_size, "bold"))
    f"{title}:", font=(font_family, font_size, "bold")
    )
    self.value_label = sg.Text( self.value_label = sg.Text(
    f"- {self.__metric}", f"- {self.__metric}",
    font=(font_family, font_size, "bold"), font=(font_family, font_size, "bold"),
    ......
    gui/widgets/plots.py → respir_os/gui/widgets/plots.py
    View file @ 0658772c
    ...@@ -4,10 +4,10 @@ from typing import Dict ...@@ -4,10 +4,10 @@ from typing import Dict
    import matplotlib.pyplot as plt import matplotlib.pyplot as plt
    import PySimpleGUI as sg import PySimpleGUI as sg
    from common.ipc import Topic
    from gui.component import Component
    from gui.ipc import ZMQEvent
    from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
    from respir_os.common.ipc import Topic
    from respir_os.gui.component import Component
    from respir_os.gui.ipc import ZMQEvent
    FIGURE_SECONDS = 20 # seconds FIGURE_SECONDS = 20 # seconds
    SAMPLE_PERIOD = 0.02 # samples SAMPLE_PERIOD = 0.02 # samples
    ......
    gui/widgets/sliders.py → respir_os/gui/widgets/sliders.py
    View file @ 0658772c
    from typing import Dict, Tuple, Union from typing import Dict, Tuple, Union
    import PySimpleGUI as sg import PySimpleGUI as sg
    from gui.component import Component from respir_os.gui.component import Component
    class NumericSlider(Component): class NumericSlider(Component):
    ......
    scripts/run deleted 100755 → 0
    View file @ 145aaaf0
    #!/bin/bash
    taskset -c 0 python -m controls & CONTROLS_PID=$!
    taskset -c 1 python -m gui & GUI_PID=$!
    taskset -c 2 python -m api & API_PID=$!
    trap finish SIGINT
    finish() {
    kill -9 $CONTROLS_PID
    kill -9 $GUI_PID
    kill -9 $API_PID
    exit
    }
    sleep infinity
    scripts/run-dev deleted 100644 → 0
    View file @ 145aaaf0
    #!/bin/bash
    export ENV=development
    source run
    scripts/run-test deleted 100644 → 0
    View file @ 145aaaf0
    #!/bin/bash
    export ENV=test
    source run
    setup.py deleted 100644 → 0
    View file @ 145aaaf0
    import pathlib
    import setuptools
    HERE = pathlib.Path(__file__).parent
    AUTHORS = (HERE / "AUTHORS").read_text()
    README = (HERE / "README.md").read_text()
    setuptools.setup(
    name="respir-os",
    version="1.0.0",
    author=", ".join(AUTHORS.splitlines()),
    license="LGPL-3",
    description="""
    Open design and implementation of a low-cost ventilator for COVID-19
    patients.
    """,
    long_description=README,
    long_description_content_type="text/markdown",
    classifiers=[
    "Programming Language :: Python :: 3.8",
    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
    "Intended Audience :: Healthcare Industry",
    "Natural Language :: Spanish",
    "Operating System :: Unix",
    ],
    packages=["controls", "gui", "api"],
    python_requires=">=3.8.6",
    install_requires=[
    "flask",
    "flask-socketio",
    "pigpio",
    "pysimplegui",
    "matplotlib",
    "numpy",
    "gevent",
    "pyzmq",
    ],
    scripts=["scripts/run", "scripts/run-dev", "scripts/run-test"],
    )
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