diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 1260f2c9d..66389fd5b 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -6,20 +6,35 @@ version: 2 updates: # Maintain dependencies for the documentation system - - package-ecosystem: "pip" - directory: "/documentation" + - package-ecosystem: 'pip' + directory: '/documentation' schedule: - interval: "monthly" + interval: 'monthly' + + - package-ecosystem: 'pip' + directory: '/controller' + schedule: + interval: 'monthly' + + - package-ecosystem: 'pip' + directory: '/segmenter' + schedule: + interval: 'monthly' + + - package-ecosystem: 'npm' + directory: '/node-red' + schedule: + interval: 'monthly' # Maintain dependencies for the Docker container to serve the documentation - - package-ecosystem: "docker" + - package-ecosystem: 'docker' # Look for a Dockerfile in the `documentation` diectory - directory: "/documentation" + directory: '/documentation' schedule: - interval: "monthly" + interval: 'monthly' # Maintain dependencies for GitHub Actions - - package-ecosystem: "github-actions" - directory: "/" + - package-ecosystem: 'github-actions' + directory: '/' schedule: - interval: "monthly" + interval: 'monthly' diff --git a/.github/workflows/build-segmenter.yml b/.github/workflows/build-segmenter.yml index 8a41dcd1a..83712426b 100644 --- a/.github/workflows/build-segmenter.yml +++ b/.github/workflows/build-segmenter.yml @@ -1,4 +1,4 @@ -name: Build Docker container image for the segmenter +name: Build the segmenter on: push: @@ -32,6 +32,31 @@ env: PUSH_IMAGE: ${{ (github.event_name == 'pull_request' && !github.event.pull_request.head.repo.fork) || github.event_name == 'push' || github.event_name == 'push tag' }} jobs: + ci-checks: + runs-on: ubuntu-24.04-arm + steps: + - uses: actions/checkout@v4 + + - name: Install poetry + run: pipx install poetry==2.1.2 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.11' + cache: 'poetry' + cache-dependency-path: | + segmenter/poetry.lock + + - name: Install build dependencies + working-directory: ./segmenter + run: | + poetry install --with dev + + - name: Run checks + working-directory: ./segmenter + run: poetry run poe check + build-container-image: permissions: contents: read diff --git a/.gitignore b/.gitignore index 76ddad8a3..9112ce0b6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,27 +1,12 @@ -# General +# macOS .DS_Store -*.dll -*.log -*.so -*.swp -export -img -tmp # Python -/*.py[cod] -/__pycache__ -/.benchmark -/.coverage* -/.pytest_cache +__pycache__ # npm node_modules -# Node-Red -/.main.json.backup -/flow_backup.json - # PlanktoScope config files hardware.json config.json diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 3a964acb7..29f1ecaa7 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -7,7 +7,8 @@ "esbenp.prettier-vscode", "charliermarsh.ruff", "editorconfig.editorconfig", - "dbaeumer.vscode-eslint" + "dbaeumer.vscode-eslint", + "ms-python.mypy-type-checker" ], // List of extensions recommended by VSCodium that should not be recommended for users of this workspace. diff --git a/controller/adafruithat/planktoscope/mqtt.py b/controller/adafruithat/planktoscope/mqtt.py index 2d153032d..7b665d887 100644 --- a/controller/adafruithat/planktoscope/mqtt.py +++ b/controller/adafruithat/planktoscope/mqtt.py @@ -70,6 +70,7 @@ # We can use collections.deque https://docs.python.org/3/library/collections.html#collections.deque import paho.mqtt.client as mqtt import json +from os import getenv # Logger library compatible with multiprocessing from loguru import logger @@ -84,7 +85,9 @@ class MQTT_Client: when creating this object """ - def __init__(self, topic, server="127.0.0.1", port=1883, name="client"): + def __init__( + self, topic, hostname=getenv("MQTT_HOSTNAME", "localhost"), port=1883, name="client" + ): # Declare the global variables command and args self.command = "" self.args = "" @@ -95,17 +98,17 @@ def __init__(self, topic, server="127.0.0.1", port=1883, name="client"): self.client = mqtt.Client() # self.client.enable_logger(logger) self.topic = topic - self.server = server + self.hostname = hostname self.port = port self.name = name self.connect() @logger.catch def connect(self): - logger.info(f"trying to connect to {self.server}:{self.port}") + logger.info(f"trying to connect to {self.hostname}:{self.port}") # TODO #104 add try: except ConnectionRefusedError: block here # This is a symptom that Mosquitto may have failed to start - self.client.connect(self.server, self.port, 60) + self.client.connect(self.hostname, self.port, 60) self.client.on_connect = self.on_connect self.client.on_subscribe = self.on_subscribe self.client.on_message = self.on_message @@ -128,7 +131,7 @@ def on_connect(self, client, userdata, flags, rc): "5: Connection refused - not authorised", ] # Print when connected - logger.success(f"{self.name} connected to {self.server}:{self.port}! - {reason[rc]}") + logger.success(f"{self.name} connected to {self.hostname}:{self.port}! - {reason[rc]}") # When connected, run subscribe() self.client.subscribe(self.topic) diff --git a/controller/planktoscopehat/planktoscope/mqtt.py b/controller/planktoscopehat/planktoscope/mqtt.py index 543e21a7c..f54d22279 100644 --- a/controller/planktoscopehat/planktoscope/mqtt.py +++ b/controller/planktoscopehat/planktoscope/mqtt.py @@ -53,6 +53,7 @@ # We can use collections.deque https://docs.python.org/3/library/collections.html#collections.deque import paho.mqtt.client as mqtt import json +from os import getenv # Logger library compatible with multiprocessing from loguru import logger @@ -67,7 +68,9 @@ class MQTT_Client: when creating this object """ - def __init__(self, topic, server="127.0.0.1", port=1883, name="client"): + def __init__( + self, topic, hostname=getenv("MQTT_HOSTNAME", "localhost"), port=1883, name="client" + ): # Declare the global variables command and args self.args = "" self.__new_message = False @@ -77,17 +80,17 @@ def __init__(self, topic, server="127.0.0.1", port=1883, name="client"): self.client = mqtt.Client() # self.client.enable_logger(logger) self.topic = topic - self.server = server + self.hostname = hostname self.port = port self.name = name self.connect() @logger.catch def connect(self): - logger.info(f"trying to connect to {self.server}:{self.port}") + logger.info(f"trying to connect to {self.hostname}:{self.port}") # TODO #104 add try: except ConnectionRefusedError: block here # This is a symptom that Mosquitto may have failed to start - self.client.connect(self.server, self.port, 60) + self.client.connect(self.hostname, self.port, 60) self.client.on_connect = self.on_connect self.client.on_subscribe = self.on_subscribe self.client.on_message = self.on_message @@ -110,7 +113,7 @@ def on_connect(self, client, userdata, flags, rc): "5: Connection refused - not authorised", ] # Print when connected - logger.success(f"{self.name} connected to {self.server}:{self.port}! - {reason[rc]}") + logger.success(f"{self.name} connected to {self.hostname}:{self.port}! - {reason[rc]}") # When connected, run subscribe() self.client.subscribe(self.topic) diff --git a/segmenter/Dockerfile b/segmenter/Dockerfile index 3da88ab23..4839852c8 100644 --- a/segmenter/Dockerfile +++ b/segmenter/Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/library/python:3.9.18-slim-bullseye +FROM docker.io/library/python:3.11-slim-bookworm # Install OS dependencies @@ -16,6 +16,8 @@ USER pi:pi RUN mkdir -p /home/pi/PlanktoScope/segmenter WORKDIR /home/pi/PlanktoScope/segmenter +ENV MQTT_HOSTNAME=host.docker.internal + # Install Python dependencies # Note: cmake is needed to install ninja which is needed to install pyproject.toml-based projects. diff --git a/segmenter/README.md b/segmenter/README.md index 838543558..1700a34c6 100644 --- a/segmenter/README.md +++ b/segmenter/README.md @@ -16,7 +16,36 @@ Currently, the simplest way to deploy the segmenter on any computer is using the ### Development -TBD +Install all dependencies including development tooling: + +```sh +poetry install --with dev +``` + +Start controller for development: + +```sh +docker ps +# copy the container id of the segmenter +docker stop + +poetry run python -u main.py +# make changes and restart +``` + +Run the code auto-formatter on the project: + +```sh +poetry run poe fmt +``` + +Run all checks (including code formatting and linting): + +```sh +poetry run poe check +``` + +We recommand using [https://code.visualstudio.com/docs/remote/ssh](https://code.visualstudio.com/docs/remote/ssh) ### Prerequisites diff --git a/segmenter/apt-packages b/segmenter/apt-packages index d306d38a4..c5d47e117 100644 --- a/segmenter/apt-packages +++ b/segmenter/apt-packages @@ -1,12 +1,8 @@ # numpy/scipy dependencies -libopenblas0 -libatlas3-base libatomic1 # opencv dependencies -libhdf5-103-1 libopenjp2-7 -libopenexr25 -libavcodec58 -libavformat58 -libswscale5 +libavcodec59 +libavformat59 +libswscale6 diff --git a/segmenter/main.py b/segmenter/main.py index d808a0cd4..fc9d2f9aa 100644 --- a/segmenter/main.py +++ b/segmenter/main.py @@ -63,9 +63,7 @@ def handler_stop_signals(signum, _): if __name__ == "__main__": logger.info("Welcome!") - logger.info( - "Initialising signals handling and sanitizing the directories (step 1/2)" - ) + logger.info("Initialising signals handling and sanitizing the directories (step 1/2)") signal.signal(signal.SIGINT, handler_stop_signals) signal.signal(signal.SIGTERM, handler_stop_signals) @@ -82,9 +80,7 @@ def handler_stop_signals(signum, _): # Starts the segmenter process logger.info("Starting the segmenter control process (step 2/2)") try: - segmenter_thread = planktoscope.segmenter.SegmenterProcess( - shutdown_event, "/home/pi/data" - ) + segmenter_thread = planktoscope.segmenter.SegmenterProcess(shutdown_event, "/home/pi/data") except Exception: logger.error("The segmenter control process could not be started") segmenter_thread = None diff --git a/segmenter/planktoscope/__init__.py b/segmenter/planktoscope/__init__.py index 92ea7a624..fb063a3ce 100644 --- a/segmenter/planktoscope/__init__.py +++ b/segmenter/planktoscope/__init__.py @@ -1,17 +1,17 @@ # Copyright (C) 2021 Romain Bazile -# +# # This file is part of the PlanktoScope software. -# +# # PlanktoScope is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. -# +# # PlanktoScope is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. -# +# # You should have received a copy of the GNU General Public License # along with PlanktoScope. If not, see . diff --git a/segmenter/planktoscope/identity.py b/segmenter/planktoscope/identity.py index 77f086be7..8e4d0973c 100644 --- a/segmenter/planktoscope/identity.py +++ b/segmenter/planktoscope/identity.py @@ -1,5 +1,6 @@ # TODO: keep this as the default path, but allow changing it with an environment variable -MACHINE_NAME_PATH = '/run/machine-name' +MACHINE_NAME_PATH = "/run/machine-name" + def load_machine_name(path=MACHINE_NAME_PATH): """Returns the machine name specified by the file at MACHINE_NAMEPATH. @@ -7,5 +8,5 @@ def load_machine_name(path=MACHINE_NAME_PATH): Returns: str: the machine name stored in the file at the path. """ - with open(path, encoding='utf-8') as file: + with open(path, encoding="utf-8") as file: return file.readline().strip() diff --git a/segmenter/planktoscope/mqtt.py b/segmenter/planktoscope/mqtt.py index e5737fdc9..7b665d887 100644 --- a/segmenter/planktoscope/mqtt.py +++ b/segmenter/planktoscope/mqtt.py @@ -1,17 +1,17 @@ # Copyright (C) 2021 Romain Bazile -# +# # This file is part of the PlanktoScope software. -# +# # PlanktoScope is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. -# +# # PlanktoScope is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. -# +# # You should have received a copy of the GNU General Public License # along with PlanktoScope. If not, see . @@ -70,6 +70,7 @@ # We can use collections.deque https://docs.python.org/3/library/collections.html#collections.deque import paho.mqtt.client as mqtt import json +from os import getenv # Logger library compatible with multiprocessing from loguru import logger @@ -84,7 +85,9 @@ class MQTT_Client: when creating this object """ - def __init__(self, topic, server="host.docker.internal", port=1883, name="client"): + def __init__( + self, topic, hostname=getenv("MQTT_HOSTNAME", "localhost"), port=1883, name="client" + ): # Declare the global variables command and args self.command = "" self.args = "" @@ -95,17 +98,17 @@ def __init__(self, topic, server="host.docker.internal", port=1883, name="client self.client = mqtt.Client() # self.client.enable_logger(logger) self.topic = topic - self.server = server + self.hostname = hostname self.port = port self.name = name self.connect() @logger.catch def connect(self): - logger.info(f"trying to connect to {self.server}:{self.port}") + logger.info(f"trying to connect to {self.hostname}:{self.port}") # TODO #104 add try: except ConnectionRefusedError: block here # This is a symptom that Mosquitto may have failed to start - self.client.connect(self.server, self.port, 60) + self.client.connect(self.hostname, self.port, 60) self.client.on_connect = self.on_connect self.client.on_subscribe = self.on_subscribe self.client.on_message = self.on_message @@ -128,9 +131,7 @@ def on_connect(self, client, userdata, flags, rc): "5: Connection refused - not authorised", ] # Print when connected - logger.success( - f"{self.name} connected to {self.server}:{self.port}! - {reason[rc]}" - ) + logger.success(f"{self.name} connected to {self.hostname}:{self.port}! - {reason[rc]}") # When connected, run subscribe() self.client.subscribe(self.topic) @@ -139,9 +140,7 @@ def on_connect(self, client, userdata, flags, rc): def on_subscribe(self, client, obj, mid, granted_qos): # Print when subscribed # TODO Fix bug when this is called outside of this init function (for example when the imager subscribe to status/pump) - logger.success( - f"{self.name} subscribed to {self.topic}! - mid:{mid} qos:{granted_qos}" - ) + logger.success(f"{self.name} subscribed to {self.topic}! - mid:{mid} qos:{granted_qos}") # Run this command when Node-RED is sending a message on the subscribed topic @logger.catch @@ -162,9 +161,7 @@ def on_message(self, client, userdata, msg): @logger.catch def on_disconnect(self, client, userdata, rc): if rc != 0: - logger.error( - f"Connection to the MQTT server is unexpectedly lost by {self.name}" - ) + logger.error(f"Connection to the MQTT server is unexpectedly lost by {self.name}") else: logger.warning(f"Connection to the MQTT server is closed by {self.name}") # TODO for now, we just log the disconnection, we need to evaluate what to do diff --git a/segmenter/planktoscope/segmenter/__init__.py b/segmenter/planktoscope/segmenter/__init__.py index d9641f0e9..5fee30219 100644 --- a/segmenter/planktoscope/segmenter/__init__.py +++ b/segmenter/planktoscope/segmenter/__init__.py @@ -69,13 +69,9 @@ "SEGMENTER_PIPELINE_SUBTRACT_CONSECUTIVE_MASKS", "False" ).lower() in ("true", "1", "t") if SUBTRACT_CONSECUTIVE_MASKS: - logger.info( - "The segmentation pipeline will subtract masks between consecutive raw frames!" - ) + logger.info("The segmentation pipeline will subtract masks between consecutive raw frames!") else: - logger.info( - "The segmentation pipeline will NOT subtract masks between consecutive raw frames!" - ) + logger.info("The segmentation pipeline will NOT subtract masks between consecutive raw frames!") ################################################################################ @@ -170,9 +166,7 @@ def _calculate_flat(self, images_list, images_number, images_root_path): # make sure image number is smaller than image list if images_number > len(images_list): - logger.error( - "The image number can't be bigger than the length of the provided list!" - ) + logger.error("The image number can't be bigger than the length of the provided list!") images_number = len(images_list) logger.debug(f"Opening {images_number} images: {images_list[:images_number]}") @@ -230,9 +224,7 @@ def _open_and_apply_flat(self, filepath, flat_ref): # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(time.monotonic() - start) - image = skimage.exposure.rescale_intensity( - image, in_range=(0, 1.04), out_range="uint8" - ) + image = skimage.exposure.rescale_intensity(image, in_range=(0, 1.04), out_range="uint8") # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) logger.debug(time.monotonic() - start) logger.success("Flat calc") @@ -280,7 +272,7 @@ def _create_mask(self, img, debug_saving_path): def _get_color_info(self, bgr_img, mask): # bgr_mean, bgr_stddev = cv2.meanStdDev(bgr_img, mask=mask) # (b_channel, g_channel, r_channel) = cv2.split(bgr_img) - quartiles = [0, 0.05, 0.25, 0.50, 0.75, 0.95, 1] + # quartiles = [0, 0.05, 0.25, 0.50, 0.75, 0.95, 1] # b_quartiles = np.quantile(b_channel, quartiles) # g_quartiles = np.quantile(g_channel, quartiles) # r_quartiles = np.quantile(r_channel, quartiles) @@ -433,9 +425,7 @@ def pipe_full(conn): return len(w) == 0 img_object = io.BytesIO() - PIL.Image.fromarray(cv2.cvtColor(img, cv2.COLOR_BGR2RGB)).save( - img_object, format="JPEG" - ) + PIL.Image.fromarray(cv2.cvtColor(img, cv2.COLOR_BGR2RGB)).save(img_object, format="JPEG") logger.debug("Sending the object in the pipe!") if not pipe_full(planktoscope.segmenter.streamer.sender): planktoscope.segmenter.streamer.sender.send(img_object) @@ -484,9 +474,7 @@ def __augment_slice(dim_slice, max_dims, size=10): labels, nlabels = skimage.measure.label(mask, return_num=True) regionprops = skimage.measure.regionprops(labels) - regionprops_filtered = [ - region for region in regionprops if region.filled_area >= min_area - ] + regionprops_filtered = [region for region in regionprops if region.filled_area >= min_area] object_number = len(regionprops_filtered) logger.debug(f"Found {nlabels} labels, or {object_number} after size filtering") @@ -526,9 +514,7 @@ def __augment_slice(dim_slice, max_dims, size=10): # publish metrics about the found object self.segmenter_client.client.publish( "status/segmenter/metric", - json.dumps( - object_metadata, cls=planktoscope.segmenter.encoder.NpEncoder - ), + json.dumps(object_metadata, cls=planktoscope.segmenter.encoder.NpEncoder), ) if "objects" in self.__global_metadata: @@ -578,9 +564,7 @@ def __augment_slice(dim_slice, max_dims, size=10): def _pipe(self, ecotaxa_export): logger.info("Finding images") - images_list = self._find_files( - self.__working_path, ("JPG", "jpg", "JPEG", "jpeg") - ) + images_list = self._find_files(self.__working_path, ("JPG", "jpg", "JPEG", "jpeg")) logger.debug(f"Images found are {images_list}") images_count = len(images_list) @@ -594,7 +578,7 @@ def _pipe(self, ecotaxa_export): first_start = time.monotonic() self.__mask_to_remove = None - average = 0 + # average = 0 total_objects = 0 average_objects = 0 recalculate_flat = True @@ -606,9 +590,7 @@ def _pipe(self, ecotaxa_export): "status/segmenter", '{"status":"Calculating flat"}' ) if images_count < 10: - self._calculate_flat( - images_list[0:images_count], images_count, self.__working_path - ) + self._calculate_flat(images_list[0:images_count], images_count, self.__working_path) else: self._calculate_flat(images_list[0:10], 10, self.__working_path) @@ -627,7 +609,7 @@ def _pipe(self, ecotaxa_export): # Publish the object_id to via MQTT to Node-RED self.segmenter_client.client.publish( "status/segmenter", - f'{{"status":"Segmenting image {filename}, image {i+1}/{images_count}"}}', + f'{{"status":"Segmenting image {filename}, image {i + 1}/{images_count}"}}', ) # we recalculate the flat if the heuristics detected we should @@ -638,13 +620,9 @@ def _pipe(self, ecotaxa_export): flat = self._calculate_flat(images_list, 10, self.__working_path) elif i > (len(images_list) - 11): # We are too close to the end of the list, take the previous 10 images instead of the next 10 - flat = self._calculate_flat( - images_list[i - 10 : i], 10, self.__working_path - ) + flat = self._calculate_flat(images_list[i - 10 : i], 10, self.__working_path) else: - flat = self._calculate_flat( - images_list[i : i + 10], 10, self.__working_path - ) + flat = self._calculate_flat(images_list[i : i + 10], 10, self.__working_path) # noqa: F841 if self.__save_debug_img: self._save_image( self.__flat, @@ -667,7 +645,7 @@ def _pipe(self, ecotaxa_export): os.makedirs(self.__working_debug_path) start = time.monotonic() - logger.info(f"Starting work on {name}, image {i+1}/{images_count}") + logger.info(f"Starting work on {name}, image {i + 1}/{images_count}") img = self._open_and_apply_flat( os.path.join(self.__working_path, images_list[i]), self.__flat @@ -713,7 +691,7 @@ def _pipe(self, ecotaxa_export): total_duration = (time.monotonic() - first_start) / 60 logger.success( - f"{images_count} images done in {total_duration} minutes, or an average of {average_time}s per image or {total_duration*60/images_count}s per image" + f"{images_count} images done in {total_duration} minutes, or an average of {average_time}s per image or {total_duration * 60 / images_count}s per image" ) logger.success( f"We also found {total_objects} objects, or an average of {total_objects / (total_duration * 60)}objects per second" @@ -733,9 +711,7 @@ def _pipe(self, ecotaxa_export): else: logger.info("There are no objects to export") else: - logger.info( - "We are not creating the ecotaxa output archive for this folder" - ) + logger.info("We are not creating the ecotaxa output archive for this folder") # cleanup # we're done free some mem @@ -781,13 +757,9 @@ def segment_list(self, path_list: list, force=False, ecotaxa_export=True): if os.path.exists(os.path.join(path, "metadata.json")): # The file exists, let's check if we force or not # we also need to check for the presence of done.txt in each folder - logger.debug( - f"{path}: Checking for the presence of done.txt or forcing({force})" - ) + logger.debug(f"{path}: Checking for the presence of done.txt or forcing({force})") if os.path.exists(os.path.join(path, "done.txt")) and not force: - logger.debug( - f"Moving to the next folder, {path} has already been segmented" - ) + logger.debug(f"Moving to the next folder, {path} has already been segmented") else: # forcing, let's gooooo try: @@ -799,9 +771,7 @@ def segment_list(self, path_list: list, force=False, ecotaxa_export=True): logger.debug(f"Moving to the next folder, {path} has no metadata.json") if exception is None: # Publish the status "Done" to via MQTT to Node-RED - self.segmenter_client.client.publish( - "status/segmenter", '{"status":"Done"}' - ) + self.segmenter_client.client.publish("status/segmenter", '{"status":"Done"}') else: self.segmenter_client.client.publish( "status/segmenter", @@ -933,11 +903,7 @@ def treat_message(self): # {"action":"segment"} if "settings" in last_message: # force rework of already done folder - force = ( - last_message["settings"]["force"] - if "force" in last_message - else False - ) + force = last_message["settings"]["force"] if "force" in last_message else False # parse folders recursively starting from the given parameter recursive = ( @@ -948,9 +914,7 @@ def treat_message(self): # generate ecotaxa output archive ecotaxa_export = ( - last_message["settings"]["ecotaxa"] - if "ecotaxa" in last_message - else True + last_message["settings"]["ecotaxa"] if "ecotaxa" in last_message else True ) if "keep" in last_message["settings"]: @@ -965,9 +929,7 @@ def treat_message(self): path = last_message["path"] if "path" in last_message else None # Publish the status "Started" to via MQTT to Node-RED - self.segmenter_client.client.publish( - "status/segmenter", '{"status":"Started"}' - ) + self.segmenter_client.client.publish("status/segmenter", '{"status":"Started"}') if path: if recursive: self.segment_all(path, force, ecotaxa_export) @@ -980,24 +942,16 @@ def treat_message(self): logger.info("The segmentation has been interrupted.") # Publish the status "Interrupted" to via MQTT to Node-RED - self.segmenter_client.client.publish( - "status/segmenter", '{"status":"Interrupted"}' - ) + self.segmenter_client.client.publish("status/segmenter", '{"status":"Interrupted"}') elif last_message["action"] == "update_config": - logger.error( - "We can't update the configuration while we are segmenting." - ) + logger.error("We can't update the configuration while we are segmenting.") # Publish the status "Interrupted" to via MQTT to Node-RED - self.segmenter_client.client.publish( - "status/segmenter", '{"status":"Busy"}' - ) + self.segmenter_client.client.publish("status/segmenter", '{"status":"Busy"}') elif last_message["action"] != "": - logger.warning( - f"We did not understand the received request {last_message}" - ) + logger.warning(f"We did not understand the received request {last_message}") ################################################################################ # While loop for capturing commands from Node-RED @@ -1005,9 +959,7 @@ def treat_message(self): @logger.catch def run(self): """This is the function that needs to be started to create a thread""" - logger.info( - f"The segmenter control thread has been started in process {os.getpid()}" - ) + logger.info(f"The segmenter control thread has been started in process {os.getpid()}") # MQTT Service connection self.segmenter_client = planktoscope.mqtt.MQTT_Client( @@ -1019,22 +971,16 @@ def run(self): logger.info("Setting up the streaming server thread") address = ("", 8001) - fps = 0.5 + # fps = 0.5 refresh_delay = 3 # was 1/fps - handler = functools.partial( - planktoscope.segmenter.streamer.StreamingHandler, refresh_delay - ) + handler = functools.partial(planktoscope.segmenter.streamer.StreamingHandler, refresh_delay) try: server = planktoscope.segmenter.streamer.StreamingServer(address, handler) except Exception as e: - logger.exception( - f"An exception has occurred when starting up the segmenter: {e}" - ) + logger.exception(f"An exception has occurred when starting up the segmenter: {e}") raise e - self.streaming_thread = threading.Thread( - target=server.serve_forever, daemon=True - ) + self.streaming_thread = threading.Thread(target=server.serve_forever, daemon=True) # start streaming only when needed self.streaming_thread.start() diff --git a/segmenter/planktoscope/segmenter/ecotaxa.py b/segmenter/planktoscope/segmenter/ecotaxa.py index b3991160b..ab3ece883 100644 --- a/segmenter/planktoscope/segmenter/ecotaxa.py +++ b/segmenter/planktoscope/segmenter/ecotaxa.py @@ -240,7 +240,7 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False # sometimes the camera resolution is not exported as string if not isinstance(metadata["acq_camera_resolution"], str): metadata["acq_camera_resolution"] = ( - f'{metadata["acq_camera_resolution"][0]}x{metadata["acq_camera_resolution"][1]}' + f"{metadata['acq_camera_resolution'][0]}x{metadata['acq_camera_resolution'][1]}" ) # let's go! @@ -277,14 +277,10 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False # add the tsv to the archive archive.writestr( tsv_filename, - io.BytesIO( - tsv_content.to_csv(sep="\t", encoding="utf-8", index=False).encode() - ).read(), + io.BytesIO(tsv_content.to_csv(sep="\t", encoding="utf-8", index=False).encode()).read(), ) if keep_files: tsv_file = os.path.join(image_base_path, tsv_filename) - tsv_content.to_csv( - path_or_buf=tsv_file, sep="\t", encoding="utf-8", index=False - ) + tsv_content.to_csv(path_or_buf=tsv_file, sep="\t", encoding="utf-8", index=False) logger.success("Ecotaxa archive is ready!") return 1 diff --git a/segmenter/planktoscope/segmenter/encoder.py b/segmenter/planktoscope/segmenter/encoder.py index 9aafbbe62..3655d41e7 100644 --- a/segmenter/planktoscope/segmenter/encoder.py +++ b/segmenter/planktoscope/segmenter/encoder.py @@ -1,17 +1,17 @@ # Copyright (C) 2021 Romain Bazile -# +# # This file is part of the PlanktoScope software. -# +# # PlanktoScope is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. -# +# # PlanktoScope is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. -# +# # You should have received a copy of the GNU General Public License # along with PlanktoScope. If not, see . diff --git a/segmenter/planktoscope/segmenter/operations.py b/segmenter/planktoscope/segmenter/operations.py index 624e4100e..8fec3272b 100644 --- a/segmenter/planktoscope/segmenter/operations.py +++ b/segmenter/planktoscope/segmenter/operations.py @@ -1,17 +1,17 @@ # Copyright (C) 2021 Romain Bazile -# +# # This file is part of the PlanktoScope software. -# +# # PlanktoScope is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. -# +# # PlanktoScope is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. -# +# # You should have received a copy of the GNU General Public License # along with PlanktoScope. If not, see . @@ -72,9 +72,7 @@ def simple_threshold(img): logger.debug("Simple threshold calc") # img_hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV) img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY) - ret, mask = cv2.threshold( - img_gray, 127, 255, cv2.THRESH_BINARY_INV + cv2.THRESH_TRIANGLE - ) + ret, mask = cv2.threshold(img_gray, 127, 255, cv2.THRESH_BINARY_INV + cv2.THRESH_TRIANGLE) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(time.monotonic() - start) diff --git a/segmenter/planktoscope/segmenter/streamer.py b/segmenter/planktoscope/segmenter/streamer.py index aa1758848..20774a7a7 100644 --- a/segmenter/planktoscope/segmenter/streamer.py +++ b/segmenter/planktoscope/segmenter/streamer.py @@ -1,17 +1,17 @@ # Copyright (C) 2021 Romain Bazile -# +# # This file is part of the PlanktoScope software. -# +# # PlanktoScope is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. -# +# # PlanktoScope is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. -# +# # You should have received a copy of the GNU General Public License # along with PlanktoScope. If not, see . @@ -21,7 +21,6 @@ import socketserver import http.server -import threading import multiprocessing # assert_new_image = threading.Condition() @@ -50,9 +49,7 @@ def do_GET(self): self.send_header("Age", 0) self.send_header("Cache-Control", "no-cache, private") self.send_header("Pragma", "no-cache") - self.send_header( - "Content-Type", "multipart/x-mixed-replace; boundary=FRAME" - ) + self.send_header("Content-Type", "multipart/x-mixed-replace; boundary=FRAME") self.end_headers() try: @@ -61,10 +58,8 @@ def do_GET(self): logger.debug("Got a new object in the pipe!") try: file = receiver.recv() - except EOFError as e: - logger.error( - "Pipe has been closed, nothing is left here, let's die" - ) + except EOFError: + logger.error("Pipe has been closed, nothing is left here, let's die") break frame = file.getvalue() # TODO #101 insert try block here to catch ConnectionResetError: [Errno 104] Connection reset by peer @@ -78,7 +73,7 @@ def do_GET(self): else: time.sleep(0.2) - except BrokenPipeError as e: + except BrokenPipeError: logger.info(f"Removed streaming client {self.client_address}") else: self.send_error(404) diff --git a/segmenter/poetry.lock b/segmenter/poetry.lock index 0ca3de4e1..958a3067e 100644 --- a/segmenter/poetry.lock +++ b/segmenter/poetry.lock @@ -15,14 +15,14 @@ files = [ [[package]] name = "imageio" -version = "2.33.0" +version = "2.37.0" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" groups = ["main"] files = [ - {file = "imageio-2.33.0-py3-none-any.whl", hash = "sha256:d580d6576d0ae39c459a444a23f6f61fe72123a3df2264f5fce8c87784a4be2e"}, - {file = "imageio-2.33.0.tar.gz", hash = "sha256:39999d05eb500089e60be467dd7d618f56e142229b44c3961c2b420eeb538d7e"}, + {file = "imageio-2.37.0-py3-none-any.whl", hash = "sha256:11efa15b87bc7871b61590326b2d635439acc321cf7f8ce996f812543ce10eed"}, + {file = 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