Merge pull request #3 from JinneGeelen/feature/v2

Merge feature/v2

.gitignore

@@ -0,0 +1,2 @@
+ui/dist
+ui/node_modules

Installation_CameraModules.md

@@ -0,0 +1,21 @@
+# Installation Camera Modules
+
+1. Download the [custom camera image](4TU?) file to build the camera module operating system on the SD cart. 
+Note! The camera modules are installed one-by-one. Finish all steps for camA before you continue to install camB.
+2. Add the custom image to one of the SD carts with [Raspberry Pi Imager](https://www.raspberrypi.com/software/)
+3. Connect power supply and insert the SD cart into the Pi
+4. Change the hostname from 'cameraX' to the preferred incremental name in order of installation.
+5. Check/Choose/Fix the IP address of the module (TBD)
+6. Choose prefererred username and password for your controller
+    1. Enter `sudo raspi-config` in a terminal window
+    2. Select `Change user password`
+    The default user on Raspberry Pi OS is `pi` with the password `raspberry`. You can change that here.
+    3. Set the visible name for this Pi on a network
+4. Add Remote Access
+    1. Enter `sudo raspi-config` in a terminal window
+    2. Select Interfacing Options
+    3. Navigate to and select SSH
+    4. Choose `Yes`
+    5. Select `Ok`
+    6. Choose `Finish`
+5. Enable/disable the CSI camera interface.

Installation_Controller.md

@@ -0,0 +1,23 @@
+# Installation Controller
+
+1. Download the [custom controller image](4TU?) file to build the controller operating system on the SD cart.
+2. Add the custom image to one of the SD carts with [Raspberry Pi Imager](https://www.raspberrypi.com/software/)
+3. Connect power supply and insert the SD cart into the Pi
+4. Choose prefererred username and password for your controller
+    1. Enter `sudo raspi-config` in a terminal window
+    2. Select `Change user password`
+    The default user on Raspberry Pi OS is `pi` with the password `raspberry`. You can change that here.
+    3. Set the visible name for this Pi on a network
+3. Add WiFi settings
+    1. Enter `sudo raspi-config` in a terminal window
+    2. Select Networking Options
+    3. Navigate to and select WiFi Settings
+    4. Fill in the credentials of your WiFi network
+4. Add Remote Access
+    1. Enter `sudo raspi-config` in a terminal window
+    2. Select Interfacing Options
+    3. Navigate to and select SSH
+    4. Choose `Yes`
+    5. Select `Ok`
+    6. Choose `Finish`
+5. Enable/disable the CSI camera interface.

api/Dockerfile

@@ -0,0 +1,12 @@
+FROM python:3.9-buster
+
+RUN apt-get update && apt-get install -y gcc libpq-dev
+
+WORKDIR /app
+
+COPY ./requirements.txt /app/requirements.txt
+RUN pip install --no-cache-dir --upgrade -r /app/requirements.txt
+
+COPY . /app
+
+CMD ["uvicorn", "app:app", "--host", "0.0.0.0", "--port", "80"]

controller/app.py → api/app.py

@@ -1,5 +1,4 @@
 import databases
-import uvicorn
 import logging
 
 from starlette.applications import Starlette
@@ -12,7 +11,7 @@
 from api import cameras, diagnostic_results, diagnostics, participants, recordings, studies
 from db import get_db, init_tables
 from controllers import camera_controller
-from config import DEBUG, DATABASE_URL, PORT
+from config import DEBUG, DATABASE_URL
 
 
 # Set up logging level globally
@@ -30,17 +29,17 @@
                    allow_headers=['*'])
 
 # Mount all the different API's
-app.mount('/v1/cameras', cameras)
-app.mount('/v1/diagnostic_results', diagnostic_results)
-app.mount('/v1/diagnostics', diagnostics)
-app.mount('/v1/participants', participants)
-app.mount('/v1/recordings', recordings)
-app.mount('/v1/studies', studies)
+app.mount('/api/cameras', cameras)
+app.mount('/api/diagnostic_results', diagnostic_results)
+app.mount('/api/diagnostics', diagnostics)
+app.mount('/api/participants', participants)
+app.mount('/api/recordings', recordings)
+app.mount('/api/studies', studies)
 
 
 # Set up OpenAPI schema
 schemas = SchemaGenerator(
-    {"openapi": "3.0.0", "info": {"title": "PiCam Controller API", "version": "1.0"}}
+    {"openapi": "3.0.0", "info": {"title": "ML-MoCap Controller API", "version": "1.0"}}
 )
 
 
@@ -61,7 +60,3 @@ async def startup():
 @app.on_event("shutdown")
 async def shutdown():
     await db.disconnect()
-
-# Start the application
-if __name__ == '__main__':
-    uvicorn.run(app, host='0.0.0.0', port=PORT)

controller/config/config.py → api/config/config.py

@@ -5,7 +5,5 @@
 config = Config('.venv')
 
 DEBUG = config('DEBUG', cast=bool, default=False)
-PORT = config('PORT', cast=int)
-LOCAL_STORAGE_PATH = config('LOCAL_STORAGE_PATH', cast=str)
-REMOTE_STORAGE_PATH = config('REMOTE_STORAGE_PATH', cast=str)
+STORAGE_PATH = config('STORAGE_PATH', cast=str)
 DATABASE_URL = config('DATABASE_URL', cast=DatabaseURL)

controller/controllers/recordings.py → api/controllers/recordings.py

@@ -12,7 +12,7 @@
 from rx.subject import Subject
 
 from db import get_db, metadata
-from config import LOCAL_STORAGE_PATH, REMOTE_STORAGE_PATH
+from config import STORAGE_PATH
 
 from controllers.controller import Controller
 from controllers.participants import participant_controller
@@ -21,13 +21,8 @@
 
 from gpiozero import LED
 
-#trigger for TMSi Porti, pin1 = 3.3V (GND = pin6)
-trigger = LED("GPIO21") #LED("BOARD40")
-led_red = LED("GPIO5") #LED("BOARD29")
-led_yellow = LED("GPIO6") #LED("BOARD31")
-led_green = LED("GPIO13") #LED("BOARD33")
-led_blue = LED("GPIO19") #LED("BOARD35")
-led_white = LED("GPIO26") #LED("BOARD")
+# trigger for TMSi Porti, pin1 = 3.3V (GND = pin6)
+trigger = LED("GPIO21")  # LED("BOARD40")
 
 logging.basicConfig(level=logging.DEBUG,
                     format='%(relativeCreated)6d %(threadName)s %(message)s')
@@ -91,38 +86,33 @@ async def get_recording_metadata(self, recording):
     async def get_recording_path(self, recording):
         participant = await participant_controller.get(recording.get('participant_id'))
         study = await studies_controller.get(participant.get('study_id'))
-        path = '{}_{}_{}'.format(study.get('name'),
+        path = '{}/{}/{}'.format(study.get('name'),
                                  participant.get('number'),
                                  recording.get('name'))
 
         return path.replace(' ', '_').replace(':', '_').replace('-', '_')
 
-    async def get_local_storage_path(self, recording):
+    async def get_storage_path(self, recording):
         recording_path = await self.get_recording_path(recording)
-        return '{}/{}'.format(LOCAL_STORAGE_PATH, recording_path)
-
-    async def get_remote_storage_path(self, recording):
-        recording_path = await self.get_recording_path(recording)
-        return '{}/{}'.format(REMOTE_STORAGE_PATH, recording_path)
+        return '{}/{}'.format(STORAGE_PATH, recording_path)
 
     async def get_camera_file_path(self, recording, camera_id):
-        local_path = await self.get_local_storage_path(recording)
+        local_path = await self.get_storage_path(recording)
 
         camera = await camera_controller.get(camera_id)
-        return '{}_{}.mp4'.format(local_path, camera.get('name', camera_id).replace(' ', '_'))
+        return '{}/{}.mp4'.format(local_path, camera.get('name', camera_id).replace(' ', '_'))
 
-#new start
-    async def sendtrigger(self, recording):
-        start_time = recording.get('start_time')
+    def send_trigger(self, recording):
+        start_time = datetime.fromisoformat(recording.get('start_time'))
         current_time = datetime.now().astimezone()
 
-        while current_time < start_time and self.recording:
+        while current_time < start_time:
             time.sleep(0.001)
             current_time = datetime.now().astimezone()
+
         trigger.on()
         time.sleep(2)
         trigger.off()
-#new end
 
     async def start(self, recording_id):
         async with self.db.transaction():
@@ -145,11 +135,11 @@ async def start(self, recording_id):
             recording['cameras_recorded'] = cameras_recorded
             recording = await self.update(recording)
 
-            #send trigger to TMSi Porti
-            thread = threading.Thread(
-                target=self.sendtrigger, args=(recording), daemon=True)
+            # send trigger to TMSi Porti
+            thread = threading.Thread(target=self.send_trigger,
+                                      args=[recording], daemon=True)
             thread.start()
-            
+
             return recording
 
     async def stop(self, recording_id):
@@ -196,21 +186,23 @@ async def process(self, recording_id):
             if not recording:
                 return
 
-            local_storage_path = await self.get_local_storage_path(recording)
-            remote_storage_path = await self.get_remote_storage_path(recording)
+            storage_path = await self.get_storage_path(recording)
 
-            if not os.path.exists(remote_storage_path):
-                os.makedirs(remote_storage_path)
+            if not os.path.exists(storage_path):
+                os.makedirs(storage_path)
 
             recording_metadata = await self.get_recording_metadata(recording)
-            metadata_path = '{}/metadata.json'.format(remote_storage_path)
+            metadata_path = '{}/metadata.json'.format(storage_path)
 
             with open(metadata_path, 'w') as file:
                 file.write(json.dumps(recording_metadata, indent=2))
 
             cameras_processing = await camera_controller.send_command({
                 'event': 'process_recording',
-                'data': recording,
+                'data': {
+                    'recording': recording,
+                    'storage_path': storage_path,
+                },
             })
 
             recording['cameras_processing'] = cameras_processing
@@ -222,16 +214,6 @@ async def process(self, recording_id):
 
     async def processed(self, recording_id, camera_id):
         recording = await self.get(recording_id)
-        camera = await camera_controller.get(camera_id)
-
-        source = await self.get_camera_file_path(recording, camera_id)
-        base_path = await self.get_remote_storage_path(recording)
-        dest = '{}/{}.mp4'.format(base_path, camera.get('name', camera_id))
-
-        thread = threading.Thread(
-            target=self.upload, args=(source, dest), daemon=True)
-        thread.start()
-
         async with self.db.transaction():
             await self.db.execute('LOCK TABLE recordings IN SHARE ROW EXCLUSIVE MODE')
 
@@ -248,11 +230,6 @@ async def processed(self, recording_id, camera_id):
 
         return recording
 
-    def upload(self, source, dest):
-        logger.info('Upload {} to {}'.format(source, dest))
-        shutil.move(source, dest)
-        logger.info('Done uploading {}'.format(dest))
-
     async def get_all(self):
         query = recordings.select()
         results = await self.db.fetch_all(query)

api/requirements.txt

@@ -0,0 +1,12 @@
+RPi.GPIO
+databases
+uvicorn[standard]
+starlette
+sqlalchemy
+asyncpg
+pyyaml
+rx
+psycopg2
+shortuuid
+gpiozero
+

camera/Dockerfile

@@ -1,5 +1,13 @@
-FROM raspbian/stretch
+FROM balenalib/raspberry-pi-python:3.7-buster
 
-COPY camera camera
+WORKDIR /app
 
-CMD [ "./camera" ]
+ENV READTHEDOCS=True
+
+COPY ./requirements.txt /app/requirements.txt
+RUN pip install --no-cache-dir --upgrade -r /app/requirements.txt
+RUN apt update && apt install -y gpac --fix-missing
+
+COPY . /app
+
+CMD ["python3", "app.py"]