From bfb2d89186073193d55642d4624723ef5765be00 Mon Sep 17 00:00:00 2001 From: MDesktop <146254978+MDesktop@users.noreply.github.com> Date: Thu, 3 Apr 2025 21:43:38 +0200 Subject: [PATCH 01/18] alligner --- src/data/accel/hbk/Accelerometer.py | 5 +- src/data/accel/hbk/alligner.py | 142 ++++++++++++++++++ src/experiment_2.py | 47 ++++++ tests/data/accel/hbk/test_accelerometer.py | 14 +- tests/data/accel/hbk/test_alligner.py | 162 +++++++++++++++++++++ 5 files changed, 361 insertions(+), 9 deletions(-) create mode 100644 src/data/accel/hbk/alligner.py create mode 100644 src/experiment_2.py create mode 100644 tests/data/accel/hbk/test_alligner.py diff --git a/src/data/accel/hbk/Accelerometer.py b/src/data/accel/hbk/Accelerometer.py index 3cd12bd..3713696 100644 --- a/src/data/accel/hbk/Accelerometer.py +++ b/src/data/accel/hbk/Accelerometer.py @@ -58,8 +58,7 @@ def _process_message(self, msg): try: raw_payload = msg.payload - # Extract metadata - # We know that the first 2 bytes tells the length of the descriptor + # The first 2 bytes tells the length of the descriptor descriptor_length = struct.unpack(" np.ndarray: + """ + Extracts a specified number of aligned samples from all channels. + + This method: + 1. Uses `find_continuous_key_groups()` to determine batch size and group keys into continuous aligned blocks. + 2. Searches for the first key group that contains enough samples. + 3. Collects aligned samples across all channels. + 4. Cleans up old and used data from each channel's buffer. + + Parameters: + requested_samples (int): The total number of samples to extract across all channels. + + Returns: + np.ndarray: A 2D NumPy array of shape (channels, requested_samples) containing aligned data. + Returns an empty array if alignment is not possible. + """ + with self._lock: + batch_size, key_groups = self.find_continuous_key_groups() + print("Keys",key_groups) + if batch_size is None or not key_groups: + return np.empty((0, len(self.channels)), dtype=np.float32) + + # Pick the first group that gives us enough samples + for group in key_groups: + total_samples = len(group) * batch_size + if total_samples >= requested_samples: + aligned_data = [] + samples_collected = 0 + + for key in group: + entries = [list(ch.data_map[key]) for ch in self.channels] + for i in range(batch_size): + if samples_collected >= requested_samples: + break + aligned_data.append([entry[i] for entry in entries]) + samples_collected += 1 + if samples_collected >= requested_samples: + break + + # Delete used and older data + for ch in self.channels: + for k in list(ch.data_map.keys()): + if k < group[0]: + del ch.data_map[k] + elif k in group: + for _ in range(min(requested_samples, len(ch.data_map[k]))): + ch.data_map[k].popleft() + if not ch.data_map[k]: + del ch.data_map[k] + + aligned_array = np.array(aligned_data, dtype=np.float32).T + print(f"Aligned shape: {aligned_array.shape}") + return aligned_array + + # No group had enough samples + return np.empty((0, len(self.channels)), dtype=np.float32) + + diff --git a/src/experiment_2.py b/src/experiment_2.py new file mode 100644 index 0000000..3162063 --- /dev/null +++ b/src/experiment_2.py @@ -0,0 +1,47 @@ +import time +import numpy as np # pylint: disable=unused-import +import uuid + +# Project imports +from data.sources.mqtt import setup_mqtt_client, load_config # type: ignore +from data.accel.hbk.alligner import Alligner # type: ignore + + +def main(): + config = load_config("config/r-pi.json") + mqtt_config = config["MQTT"] + + + topic_indexes = [0,1] # Indexes of the topics/channels to allign + + # Resolve topic names from config + all_topics = config["MQTT"]["TopicsToSubscribe"] + selected_topics = [all_topics[i] for i in topic_indexes] + + mqtt_client, _ = setup_mqtt_client(mqtt_config, topic_index=topic_indexes[0]) + mqtt_client.connect(mqtt_config["host"], mqtt_config["port"], 60) + mqtt_client.loop_start() + + # We might need to give it some time before strating allignment, + # so we make sure that there is enough data to allign. + + # pass actual topic as string + alligner = Alligner(mqtt_client, topics=selected_topics, map_size=2560) + + while True: + time.sleep(5) + data = alligner.extract(100) + if data.shape[0] == 0: + print("Not enough aligned data yet.") + else: + print(f"Extracted aligned data shape: {data.shape}\n{data}") + break + time.sleep(1) + + +if __name__ == "__main__": + main() + + + + diff --git a/tests/data/accel/hbk/test_accelerometer.py b/tests/data/accel/hbk/test_accelerometer.py index 83745f2..f139da0 100644 --- a/tests/data/accel/hbk/test_accelerometer.py +++ b/tests/data/accel/hbk/test_accelerometer.py @@ -21,7 +21,7 @@ def mqtt_client(): client.connect(mqtt_config["host"], mqtt_config["port"], 60) client.loop_start() - time.sleep(0.1) + time.sleep(0.5) yield client, selected_topic client.loop_stop() @@ -60,6 +60,8 @@ def publish_binary_samples(client, topic, start, end): result.wait_for_publish() + + def test_accelerometer_read_in_steps(client_and_topic, accelerometer_instance): """ Test that reading in steps correctly retrieves the oldest samples @@ -114,7 +116,7 @@ def test_accelerometer_read_full_fifo(client_and_topic, accelerometer_instance): publish_binary_samples(client, topic, 0, 96) total_samples = 0 - while total_samples < 96: + while total_samples < 50: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) @@ -170,7 +172,7 @@ def test_accelerometer_read_insufficient_samples(client_and_topic, accelerometer publish_binary_samples(client, topic, 0, 64) total_samples = 0 - while total_samples < 64: + while total_samples < 50: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) @@ -198,7 +200,7 @@ def test_accelerometer_appending_more_samples_than_max(client_and_topic, acceler publish_binary_samples(client, topic, 0, 224) total_samples = 0 - while total_samples < 192: + while total_samples < 100: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) @@ -224,9 +226,9 @@ def test_accelerometer_reordering_late_sample(client_and_topic, accelerometer_in # Publish middle batch (32–63) AFTER last batch publish_binary_samples(client, topic, 32, 64) - # Wait for all samples to arrive + total_samples = 0 - while total_samples < 96: # Max wait time: 5 seconds + while total_samples < 60: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) status, data = accelerometer_instance.read(96) diff --git a/tests/data/accel/hbk/test_alligner.py b/tests/data/accel/hbk/test_alligner.py new file mode 100644 index 0000000..e25bdfc --- /dev/null +++ b/tests/data/accel/hbk/test_alligner.py @@ -0,0 +1,162 @@ +import time +import json +import pytest +import struct + +import numpy as np +from data.accel.hbk.alligner import Alligner # type: ignore + + +from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE +from data.sources.mqtt import setup_mqtt_client, load_config +import uuid + + + +@pytest.fixture(scope="function") +def mqtt_client_and_config(): + config = load_config("config/test.json") + mqtt_config = config["MQTT"].copy() + mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}" + + client, _ = setup_mqtt_client(mqtt_config, topic_index=0) + client.connect(mqtt_config["host"], mqtt_config["port"], 60) + client.loop_start() + time.sleep(0.1) + + yield client, mqtt_config + + client.loop_stop() + client.disconnect() + + +@pytest.fixture(scope="function") +def mqtt_setup(): + config = load_config("config/test.json") + mqtt_config = config["MQTT"].copy() + mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}" + + # Setup MQTT client once + client, _ = setup_mqtt_client(mqtt_config, 0) + client.connect(mqtt_config["host"], mqtt_config["port"], 60) + client.loop_start() + time.sleep(0.1) + + # Extract topics manually + topics = [ + config["MQTT"]["TopicsToSubscribe"][0], + config["MQTT"]["TopicsToSubscribe"][1], + config["MQTT"]["TopicsToSubscribe"][2], + ] + + yield client, topics + + client.loop_stop() + client.disconnect() + + +def publish_samples(client, topic, values: np.ndarray, start_key: int): + """ + Publishes a list of float values to the given MQTT topic using the expected binary format. + Data is split into 32-sample batches (BATCH_SIZE). + """ + for batch_start in range(0, len(values), BATCH_SIZE): + batch_end = batch_start + BATCH_SIZE + batch_values = values[batch_start:batch_end] + data_bytes = b''.join([struct.pack(" 64 for k in remaining_keys), \ + f"Channel {i+1} still contains old data (keys <= 64): {remaining_keys}" + + + +def test_alligner_single_channel_extract_and_cleanup(mqtt_setup): + client, topics = mqtt_setup + one_topic = [topics[0]] # Use only the first topic + + alligner = Alligner(client, topics=one_topic, map_size=512) + + # Publish 128 samples to the single channel (4 batches of 32) + for key in [0, 32, 64, 96]: + publish_samples(client, topics[0], np.arange(32) + key, start_key=key) + + time.sleep(1) + + # Extract 64 samples from the single channel + extracted = alligner.extract(64) + + assert extracted.shape == (1, 64), f"Expected shape (64, 1), got {extracted.shape}" + assert np.allclose(extracted.flatten()[:5], [0, 1, 2, 3, 4]), "Unexpected values in extracted data" + + # Ensure keys 0 and 32 were removed, and 64+ remain + ch = alligner.channels[0] + with ch._lock: + remaining_keys = list(ch.data_map.keys()) + print(f"[DEBUG] Remaining keys in single channel: {remaining_keys}") + assert all(k > 32 for k in remaining_keys), f"Expected only keys > 32, but got {remaining_keys}" From d2375b8d5909b00018dcd9c3869a9c9a25f936c3 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Mon, 7 Apr 2025 12:09:19 +0200 Subject: [PATCH 02/18] Renamed Accelerometer.py to accelerometer.py --- src/data/accel/hbk/{Accelerometer.py => accelerometer.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/data/accel/hbk/{Accelerometer.py => accelerometer.py} (100%) diff --git a/src/data/accel/hbk/Accelerometer.py b/src/data/accel/hbk/accelerometer.py similarity index 100% rename from src/data/accel/hbk/Accelerometer.py rename to src/data/accel/hbk/accelerometer.py From 2fee41a27f5bcd79883a5dc017b7f4cbf74ac421 Mon Sep 17 00:00:00 2001 From: MDesktop <146254978+MDesktop@users.noreply.github.com> Date: Wed, 9 Apr 2025 19:52:15 +0200 Subject: [PATCH 03/18] config for tests --- .gitignore | 1 + config/{test.json.template => test.json} | 0 2 files changed, 1 insertion(+) rename config/{test.json.template => test.json} (100%) diff --git a/.gitignore b/.gitignore index 63a3ab8..8223b05 100644 --- a/.gitignore +++ b/.gitignore @@ -175,4 +175,5 @@ cython_debug/ # Ignore config files with credentials config/*.json +!config/test.json !config/*.json.template diff --git a/config/test.json.template b/config/test.json similarity index 100% rename from config/test.json.template rename to config/test.json From 1c26acaa224b5326b6f97d7e7584ee5c44d8a697 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Wed, 9 Apr 2025 19:56:15 +0200 Subject: [PATCH 04/18] resolved issues --- .pylintrc | 4 +-- pyproject.toml | 3 +- src/data/accel/hbk/accelerometer.py | 9 ++--- .../accel/hbk/{alligner.py => aligner.py} | 29 +++++++-------- src/data/accel/metadata_constants.py | 2 ++ src/examples/README.md | 35 +++++++++++++++++++ src/examples/__init__.py | 0 src/examples/example.py | 5 +++ src/{ => examples}/experiment_1.py | 8 ++--- src/{ => examples}/experiment_2.py | 13 +++---- tests/data/accel/hbk/test_accelerometer.py | 4 +-- .../hbk/{test_alligner.py => test_aligner.py} | 24 ++++++------- 12 files changed, 86 insertions(+), 50 deletions(-) rename src/data/accel/hbk/{alligner.py => aligner.py} (87%) create mode 100644 src/data/accel/metadata_constants.py create mode 100644 src/examples/README.md create mode 100644 src/examples/__init__.py create mode 100644 src/examples/example.py rename src/{ => examples}/experiment_1.py (91%) rename src/{ => examples}/experiment_2.py (82%) rename tests/data/accel/hbk/{test_alligner.py => test_aligner.py} (87%) diff --git a/.pylintrc b/.pylintrc index e545389..599a2bd 100644 --- a/.pylintrc +++ b/.pylintrc @@ -130,7 +130,7 @@ score=yes [REFACTORING] # Maximum number of nested blocks for function / method body -max-nested-blocks=5 +max-nested-blocks=7 # Complete name of functions that never returns. When checking for # inconsistent-return-statements if a never returning function is called then @@ -559,7 +559,7 @@ max-attributes=7 max-bool-expr=5 # Maximum number of branch for function / method body. -max-branches=12 +max-branches=15 # Maximum number of locals for function / method body. max-locals=15 diff --git a/pyproject.toml b/pyproject.toml index 4d8cae5..1e83aae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,4 +25,5 @@ requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" [tool.poetry.scripts] -experiment_1 = "src.experiment_1:main" \ No newline at end of file +experiment_1 = "src.examples.experiment_1:main" +experiment_2 = "src.examples.experiment_2:main" diff --git a/src/data/accel/hbk/accelerometer.py b/src/data/accel/hbk/accelerometer.py index 3713696..cba3d40 100644 --- a/src/data/accel/hbk/accelerometer.py +++ b/src/data/accel/hbk/accelerometer.py @@ -6,6 +6,8 @@ # Project Imports from data.accel.accelerometer import IAccelerometer from data.accel.constants import MAX_MAP_SIZE +from data.accel.metadata_constants import DESCRIPTOR_LENGTH_BYTES + class Accelerometer(IAccelerometer): def __init__( @@ -39,14 +41,14 @@ def _on_message(self, _, __, msg): def safe_process(): # This ensures that an exception does not crash the entire thread try: - self._process_message(msg) + self.process_message(msg) except Exception as e: print(f"Error processing message: {e}") threading.Thread(target=safe_process, daemon=True).start() - def _process_message(self, msg): + def process_message(self, msg): """ Processes incoming MQTT messages, extracts accelerometer data, and stores it in a dictionary of FIFO queues. @@ -58,8 +60,7 @@ def _process_message(self, msg): try: raw_payload = msg.payload - # The first 2 bytes tells the length of the descriptor - descriptor_length = struct.unpack(" np.ndarray: Extracts a specified number of aligned samples from all channels. This method: - 1. Uses `find_continuous_key_groups()` to determine batch size and group keys into continuous aligned blocks. + 1. Uses `find_continuous_key_groups()` to determine batch size + and group keys into continuous aligned blocks. 2. Searches for the first key group that contains enough samples. 3. Collects aligned samples across all channels. 4. Cleans up old and used data from each channel's buffer. @@ -95,7 +94,8 @@ def extract(self, requested_samples: int) -> np.ndarray: requested_samples (int): The total number of samples to extract across all channels. Returns: - np.ndarray: A 2D NumPy array of shape (channels, requested_samples) containing aligned data. + np.ndarray: A 2D NumPy array of shape + (channels, requested_samples) containing aligned data. Returns an empty array if alignment is not possible. """ with self._lock: @@ -108,7 +108,7 @@ def extract(self, requested_samples: int) -> np.ndarray: for group in key_groups: total_samples = len(group) * batch_size if total_samples >= requested_samples: - aligned_data = [] + aligned_data = [[] for _ in self.channels] samples_collected = 0 for key in group: @@ -116,10 +116,9 @@ def extract(self, requested_samples: int) -> np.ndarray: for i in range(batch_size): if samples_collected >= requested_samples: break - aligned_data.append([entry[i] for entry in entries]) + for ch_idx, channel_data in enumerate(entries): + aligned_data[ch_idx].append(channel_data[i]) samples_collected += 1 - if samples_collected >= requested_samples: - break # Delete used and older data for ch in self.channels: @@ -132,11 +131,9 @@ def extract(self, requested_samples: int) -> np.ndarray: if not ch.data_map[k]: del ch.data_map[k] - aligned_array = np.array(aligned_data, dtype=np.float32).T + aligned_array = np.array(aligned_data, dtype=np.float32) print(f"Aligned shape: {aligned_array.shape}") return aligned_array # No group had enough samples return np.empty((0, len(self.channels)), dtype=np.float32) - - diff --git a/src/data/accel/metadata_constants.py b/src/data/accel/metadata_constants.py new file mode 100644 index 0000000..c087fba --- /dev/null +++ b/src/data/accel/metadata_constants.py @@ -0,0 +1,2 @@ +# In messages received from /data topics. The first 2 bytes tells the length of the descriptor +DESCRIPTOR_LENGTH_BYTES = 2 diff --git a/src/examples/README.md b/src/examples/README.md new file mode 100644 index 0000000..0a71c0e --- /dev/null +++ b/src/examples/README.md @@ -0,0 +1,35 @@ +# Examples + +This directory contains examples demonstrating how to use the EXAMPLE-SHM package. + +## Installing the Package from Poetry Build + +To install the package built using `poetry`, follow these steps: + +### Step 1: Build the Package + +```bash +poetry build +``` + +This will create a .whl file in the dist/ directory, e.g., dist/cp_sens-0.1.0-py3-none-any.whl. + +### Step 2: Create and Activate a Virtual Environment + +python -m venv .venv +source .venv/bin/activate # On Linux/macOS +.\.venv\Scripts\Activate.ps1 # On Windows + +### Step 3: Install the Built Package +pip install dist/example_shm--py3-none-any.whl +Replace with the version number found in the .whl filename. (e.g 0.1.0) + + +## Running the Example + +A simple example is provided to run the main() function from experiment_1.py. + +To run this example, use: +```bash +python examples/example.py +``` diff --git a/src/examples/__init__.py b/src/examples/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/examples/example.py b/src/examples/example.py new file mode 100644 index 0000000..3abdd5f --- /dev/null +++ b/src/examples/example.py @@ -0,0 +1,5 @@ +from experiment_1 import main # pylint: disable=import-error + + +if __name__ == "__main__": + main() diff --git a/src/experiment_1.py b/src/examples/experiment_1.py similarity index 91% rename from src/experiment_1.py rename to src/examples/experiment_1.py index 2a5da5c..8bc8603 100644 --- a/src/experiment_1.py +++ b/src/examples/experiment_1.py @@ -26,7 +26,7 @@ def main(): accelerometer.data_map.clear() while True: - time.sleep(2.1) + time.sleep(1) with accelerometer.acquire_lock(): # This print to see the dictionary @@ -34,10 +34,10 @@ def main(): print(f"Key: {key} -> Data: {list(fifo)}\n") _, data = accelerometer.read(requested_samples=128) print("Data requsted", data) - #break + break - #mqtt_client.loop_stop() - #print("Data requsted", data) + mqtt_client.loop_stop() + print("Data requsted", data) if __name__ == '__main__': diff --git a/src/experiment_2.py b/src/examples/experiment_2.py similarity index 82% rename from src/experiment_2.py rename to src/examples/experiment_2.py index 3162063..dfe5266 100644 --- a/src/experiment_2.py +++ b/src/examples/experiment_2.py @@ -1,14 +1,13 @@ import time import numpy as np # pylint: disable=unused-import -import uuid # Project imports from data.sources.mqtt import setup_mqtt_client, load_config # type: ignore -from data.accel.hbk.alligner import Alligner # type: ignore +from data.accel.hbk.aligner import Aligner # type: ignore def main(): - config = load_config("config/r-pi.json") + config = load_config("config/production.json") mqtt_config = config["MQTT"] @@ -26,11 +25,11 @@ def main(): # so we make sure that there is enough data to allign. # pass actual topic as string - alligner = Alligner(mqtt_client, topics=selected_topics, map_size=2560) + aligner = Aligner(mqtt_client, topics=selected_topics, map_size=2560) while True: time.sleep(5) - data = alligner.extract(100) + data = aligner.extract(16) if data.shape[0] == 0: print("Not enough aligned data yet.") else: @@ -41,7 +40,3 @@ def main(): if __name__ == "__main__": main() - - - - diff --git a/tests/data/accel/hbk/test_accelerometer.py b/tests/data/accel/hbk/test_accelerometer.py index f139da0..6f3d05b 100644 --- a/tests/data/accel/hbk/test_accelerometer.py +++ b/tests/data/accel/hbk/test_accelerometer.py @@ -116,7 +116,7 @@ def test_accelerometer_read_full_fifo(client_and_topic, accelerometer_instance): publish_binary_samples(client, topic, 0, 96) total_samples = 0 - while total_samples < 50: + while total_samples < 60: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) @@ -144,7 +144,7 @@ def test_accelerometer_read_partial_fifo(client_and_topic, accelerometer_instanc publish_binary_samples(client, topic, 0, 64) total_samples = 0 - while total_samples < 64: + while total_samples < 60: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) diff --git a/tests/data/accel/hbk/test_alligner.py b/tests/data/accel/hbk/test_aligner.py similarity index 87% rename from tests/data/accel/hbk/test_alligner.py rename to tests/data/accel/hbk/test_aligner.py index e25bdfc..931222c 100644 --- a/tests/data/accel/hbk/test_alligner.py +++ b/tests/data/accel/hbk/test_aligner.py @@ -4,7 +4,7 @@ import struct import numpy as np -from data.accel.hbk.alligner import Alligner # type: ignore +from data.accel.hbk.aligner import Aligner # type: ignore from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE @@ -83,9 +83,9 @@ def publish_samples(client, topic, values: np.ndarray, start_key: int): -def test_alligner_continuous_block_required(mqtt_setup): +def test_aligner_continuous_block_required(mqtt_setup): client, topics = mqtt_setup - alligner = Alligner(client, topics=topics, map_size=512) + aligner = Aligner(client, topics=topics, map_size=512) # CH1 and CH2: send full keys for key in [0, 32, 64, 96, 128, 160, 192, 224]: @@ -98,7 +98,7 @@ def test_alligner_continuous_block_required(mqtt_setup): time.sleep(1.5) # Let messages arrive - aligned = alligner.extract(128) # Should use keys 96, 128, 160, 192 (128 samples) + aligned = aligner.extract(128) # Should use keys 96, 128, 160, 192 (128 samples) assert aligned.shape == (3, 128), f"Expected 128 aligned rows, got {aligned.shape}" assert np.allclose(aligned[0, :5], np.arange(5)), "Check data from channel 1" @@ -110,9 +110,9 @@ def test_alligner_continuous_block_required(mqtt_setup): -def test_alligner_extract_removes_used_and_older_data(mqtt_setup): +def test_aligner_extract_removes_used_and_older_data(mqtt_setup): client, topics = mqtt_setup - alligner = Alligner(client, topics=topics, map_size=512) + aligner = Aligner(client, topics=topics, map_size=512) # Send 5 batches (160 samples) to all 3 channels for key in [0, 32, 64, 96, 128]: @@ -122,12 +122,12 @@ def test_alligner_extract_removes_used_and_older_data(mqtt_setup): time.sleep(1) # Extract 96 samples → should consume keys 0, 32, 64 (96 samples) - aligned = alligner.extract(96) + aligned = aligner.extract(96) assert aligned.shape == (3, 96), "Expected 96 aligned samples" # Now check the internal maps - for i, ch in enumerate(alligner.channels): + for i, ch in enumerate(aligner.channels): with ch._lock: remaining_keys = list(ch.data_map.keys()) print(f"[DEBUG] Channel {i+1} remaining keys after extract: {remaining_keys}") @@ -136,11 +136,11 @@ def test_alligner_extract_removes_used_and_older_data(mqtt_setup): -def test_alligner_single_channel_extract_and_cleanup(mqtt_setup): +def test_aligner_single_channel_extract_and_cleanup(mqtt_setup): client, topics = mqtt_setup one_topic = [topics[0]] # Use only the first topic - alligner = Alligner(client, topics=one_topic, map_size=512) + aligner = Aligner(client, topics=one_topic, map_size=512) # Publish 128 samples to the single channel (4 batches of 32) for key in [0, 32, 64, 96]: @@ -149,13 +149,13 @@ def test_alligner_single_channel_extract_and_cleanup(mqtt_setup): time.sleep(1) # Extract 64 samples from the single channel - extracted = alligner.extract(64) + extracted = aligner.extract(64) assert extracted.shape == (1, 64), f"Expected shape (64, 1), got {extracted.shape}" assert np.allclose(extracted.flatten()[:5], [0, 1, 2, 3, 4]), "Unexpected values in extracted data" # Ensure keys 0 and 32 were removed, and 64+ remain - ch = alligner.channels[0] + ch = aligner.channels[0] with ch._lock: remaining_keys = list(ch.data_map.keys()) print(f"[DEBUG] Remaining keys in single channel: {remaining_keys}") From 34bec5a41918ec1924d67d139669d8a22fa1cfe8 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Thu, 10 Apr 2025 14:17:47 +0200 Subject: [PATCH 05/18] deque trimming --- .pylintrc | 2 +- config/test.json | 3 ++- src/data/accel/hbk/accelerometer.py | 13 ++++++++++--- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/.pylintrc b/.pylintrc index 599a2bd..cbf727b 100644 --- a/.pylintrc +++ b/.pylintrc @@ -562,7 +562,7 @@ max-bool-expr=5 max-branches=15 # Maximum number of locals for function / method body. -max-locals=15 +max-locals=20 # Maximum number of parents for a class (see R0901). max-parents=7 diff --git a/config/test.json b/config/test.json index 8177337..372afa3 100644 --- a/config/test.json +++ b/config/test.json @@ -1,6 +1,6 @@ { "MQTT": { - "host": "test.mosquitto.org", + "host": "mqtt.eclipseprojects.io", "port": 1883, "userId": "", "password": "", @@ -9,3 +9,4 @@ "TopicsToSubscribe": ["topicAA", "topicBB", "topicCC"] } } + diff --git a/src/data/accel/hbk/accelerometer.py b/src/data/accel/hbk/accelerometer.py index cba3d40..c243db9 100644 --- a/src/data/accel/hbk/accelerometer.py +++ b/src/data/accel/hbk/accelerometer.py @@ -72,12 +72,19 @@ def process_message(self, msg): # Store each data batch (e.g 32 samples in one message) # in the map samples_from_daq_start is used as the key for each batch with self._lock: - self.data_map[samples_from_daq_start] = deque(accel_values) + if samples_from_daq_start not in self.data_map: + self.data_map[samples_from_daq_start] = deque(accel_values) + + total_samples = sum(len(dq) for dq in self.data_map.values()) # Check if the total samples in the map exceeds the max, # then remove the oldest data batch - while sum(len(deque) for deque in self.data_map.values()) > self._map_size: + while total_samples > self._map_size: oldest_key = min(self.data_map.keys()) # Find the oldest batch - del self.data_map[oldest_key] # Remove oldest batch + oldest_deque = self.data_map[oldest_key] + oldest_deque.popleft() # Delete samples from the oldest deque + if not oldest_deque: # Remove the key/deque from the map if it's empty + del self.data_map[oldest_key] + total_samples = sum(len(dq) for dq in self.data_map.values()) print(f" Channel: {self.topic} Key: {samples_from_daq_start}, Samples: {num_samples}") except Exception as e: From cce4d376eee5651c2530b9a5d3ede5906ada1411 Mon Sep 17 00:00:00 2001 From: prasadtalasila Date: Sat, 12 Apr 2025 22:17:32 +0200 Subject: [PATCH 06/18] Fixes minor issues --- poetry.lock | 1019 +++++++++++----------------------- pyproject.toml | 4 +- src/examples/experiment_1.py | 20 +- src/examples/experiment_2.py | 7 +- 4 files changed, 348 insertions(+), 702 deletions(-) diff --git a/poetry.lock b/poetry.lock index e6bea62..57908ab 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,27 +1,15 @@ # This file is automatically @generated by Poetry 2.1.1 and 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"c8abbc2048e9c6e5526487d2d2f0d2b379e5cfc9fe5d12767c52770c296e6796" +content-hash = "4dae1746dfecc146018a0bb769eca6a3bfd4df22dec5f6cc1eff4a0bf1ae089f" diff --git a/pyproject.toml b/pyproject.toml index 1e83aae..aabc2ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "example-shm" -version = "0.1.0" -description = "" +version = "0.2.0" +description = "Demonstration for structural health monitoring of engineering structures" authors = [ "Mohamed Abdulkarim <202206332@post.au.dk>", "Prasad Talasila " diff --git a/src/examples/experiment_1.py b/src/examples/experiment_1.py index 8bc8603..0fe1c99 100644 --- a/src/examples/experiment_1.py +++ b/src/examples/experiment_1.py @@ -25,20 +25,16 @@ def main(): with accelerometer.acquire_lock(): accelerometer.data_map.clear() - while True: - time.sleep(1) - - with accelerometer.acquire_lock(): - # This print to see the dictionary - for key, fifo in sorted(accelerometer.data_map.items()): - print(f"Key: {key} -> Data: {list(fifo)}\n") - _, data = accelerometer.read(requested_samples=128) - print("Data requsted", data) - break - - mqtt_client.loop_stop() + time.sleep(10) # Allow time for data collection + with accelerometer.acquire_lock(): + # This print to see the dictionary + for key, fifo in sorted(accelerometer.data_map.items()): + print(f"Key: {key} -> Data: {list(fifo)}\n") + _, data = accelerometer.read(requested_samples=256) print("Data requsted", data) + mqtt_client.loop_stop() + mqtt_client.disconnect() if __name__ == '__main__': main() diff --git a/src/examples/experiment_2.py b/src/examples/experiment_2.py index dfe5266..c213118 100644 --- a/src/examples/experiment_2.py +++ b/src/examples/experiment_2.py @@ -1,5 +1,4 @@ import time -import numpy as np # pylint: disable=unused-import # Project imports from data.sources.mqtt import setup_mqtt_client, load_config # type: ignore @@ -11,7 +10,7 @@ def main(): mqtt_config = config["MQTT"] - topic_indexes = [0,1] # Indexes of the topics/channels to allign + topic_indexes = [0,1] # Indexes of the topics/channels to align # Resolve topic names from config all_topics = config["MQTT"]["TopicsToSubscribe"] @@ -21,8 +20,8 @@ def main(): mqtt_client.connect(mqtt_config["host"], mqtt_config["port"], 60) mqtt_client.loop_start() - # We might need to give it some time before strating allignment, - # so we make sure that there is enough data to allign. + # We might need to give it some time before strating alignment, + # so we make sure that there is enough data to align. # pass actual topic as string aligner = Aligner(mqtt_client, topics=selected_topics, map_size=2560) From aee4e0fd0081eb636cb6f676756fe4bc769232db Mon Sep 17 00:00:00 2001 From: prasadtalasila Date: Sun, 13 Apr 2025 09:34:21 +0200 Subject: [PATCH 07/18] Updates documetnation and configuration --- .coveragerc | 2 ++ README.md | 2 ++ pytest.ini | 2 +- src/data/accel/hbk/aligner.py | 3 --- src/examples/README.md | 32 ++++++++++++++++++++++++-------- 5 files changed, 29 insertions(+), 12 deletions(-) diff --git a/.coveragerc b/.coveragerc index ec5cd66..e3ff08e 100644 --- a/.coveragerc +++ b/.coveragerc @@ -4,6 +4,8 @@ omit = */venv/* */.venv/* */__init__.py + */src/data/accel/random.py + */src/examples/* [report] exclude_lines = diff --git a/README.md b/README.md index a739214..747d170 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,8 @@ poetry build # builds cp-sens package that can be published poetry run experiment_1 # run one experiment with real data ``` +The `poetry build` will create a `.whl` file in the `dist/` directory, e.g., `dist/cp_sens-0.1.0-py3-none-any.whl`. + ## Testing Write tests in the _tests_ directory. Be sure to name any new files as diff --git a/pytest.ini b/pytest.ini index 0171d98..4cb9017 100644 --- a/pytest.ini +++ b/pytest.ini @@ -3,7 +3,7 @@ minversion = 8.3 pythonpath = src src/data src/methods tests testpaths = tests -addopts = --cov=src --cov-report=term-missing --cov-report=html +addopts = --cov=src --ignore=src/examples --cov-report=term-missing --cov-report=html python_files = test_*.py log_cli=true diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index fe26356..e321e7d 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -5,7 +5,6 @@ from data.accel.hbk.accelerometer import Accelerometer # type: ignore - class Aligner: def __init__(self, mqtt_client, topics: list, map_size=44840, missing_value=np.nan): """ @@ -34,8 +33,6 @@ def __init__(self, mqtt_client, topics: list, map_size=44840, missing_value=np.n msg, acc=acc: acc.process_message(msg)) - - def find_continuous_key_groups(self): """ Determines the batch size, finds common keys, and groups them into continuous sequences. diff --git a/src/examples/README.md b/src/examples/README.md index 0a71c0e..6009825 100644 --- a/src/examples/README.md +++ b/src/examples/README.md @@ -1,8 +1,9 @@ # Examples -This directory contains examples demonstrating how to use the EXAMPLE-SHM package. +This directory contains examples demonstrating how to use +the **EXAMPLE-SHM** package. -## Installing the Package from Poetry Build +## Install the Package from Poetry Build To install the package built using `poetry`, follow these steps: @@ -12,24 +13,39 @@ To install the package built using `poetry`, follow these steps: poetry build ``` -This will create a .whl file in the dist/ directory, e.g., dist/cp_sens-0.1.0-py3-none-any.whl. +This will create a `.whl` file in the `dist/` directory, +e.g., `dist/cp_sens-0.1.0-py3-none-any.whl`. ### Step 2: Create and Activate a Virtual Environment +```py python -m venv .venv source .venv/bin/activate # On Linux/macOS .\.venv\Scripts\Activate.ps1 # On Windows +``` ### Step 3: Install the Built Package -pip install dist/example_shm--py3-none-any.whl -Replace with the version number found in the .whl filename. (e.g 0.1.0) +```py +pip install example_shm--py3-none-any.whl +``` + +Replace `` with the version number found in the `.whl` +filename. (e.g `0.1.0`). -## Running the Example +## Running the Examples -A simple example is provided to run the main() function from experiment_1.py. +There are two examples. + +* **example_1** demonstrates the use of `Accelerometer` class to extract + accelerometer measurements from MQTT data stream. +* **example_2** demonstrates the use of `Aligner` class to collect and + align accelerometer measurements from multiple MQTT data streams. + +A simple example is provided to run the `main()` function from `experiment_1.py`. To run this example, use: + ```bash -python examples/example.py +python examples/example_1.py ``` From 26d2e90d485c06aeeb36be452d6999a81e522402 Mon Sep 17 00:00:00 2001 From: prasadtalasila Date: Sun, 13 Apr 2025 10:16:06 +0200 Subject: [PATCH 08/18] Upgrades packages and python version --- .pylintrc | 6 +- poetry.lock | 547 +--------------------------------- pyproject.toml | 10 +- src/data/accel/hbk/aligner.py | 2 +- 4 files changed, 13 insertions(+), 552 deletions(-) diff --git a/.pylintrc b/.pylintrc index cbf727b..e545389 100644 --- a/.pylintrc +++ b/.pylintrc @@ -130,7 +130,7 @@ score=yes [REFACTORING] # Maximum number of nested blocks for function / method body -max-nested-blocks=7 +max-nested-blocks=5 # Complete name of functions that never returns. 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- # Create one Accelerometer per topic + seen = set() + # Create one Accelerometer per uniqe topic for topic in topics: - acc = Accelerometer(mqtt_client, topic=topic, map_size=map_size) - self.channels.append(acc) - mqtt_client.subscribe(topic, qos=1) - mqtt_client.message_callback_add(topic, lambda _, __, - msg, acc=acc: acc.process_message(msg)) + if topic not in seen: + seen.add(topic) + acc = Accelerometer(mqtt_client, topic=topic, map_size=map_size) + self.channels.append(acc) + mqtt_client.subscribe(topic, qos=1) + mqtt_client.message_callback_add(topic, lambda _, __, + msg, acc=acc: acc.process_message(msg)) def find_continuous_key_groups(self): diff --git a/src/examples/experiment_2.py b/src/examples/experiment_2.py index c213118..fea6689 100644 --- a/src/examples/experiment_2.py +++ b/src/examples/experiment_2.py @@ -10,7 +10,7 @@ def main(): mqtt_config = config["MQTT"] - topic_indexes = [0,1] # Indexes of the topics/channels to align + topic_indexes = [1,1,0,1,0] # Indexes of the topics/channels to align # Resolve topic names from config all_topics = config["MQTT"]["TopicsToSubscribe"] @@ -20,14 +20,12 @@ def main(): mqtt_client.connect(mqtt_config["host"], mqtt_config["port"], 60) mqtt_client.loop_start() - # We might need to give it some time before strating alignment, - # so we make sure that there is enough data to align. # pass actual topic as string aligner = Aligner(mqtt_client, topics=selected_topics, map_size=2560) while True: - time.sleep(5) + time.sleep(1) data = aligner.extract(16) if data.shape[0] == 0: print("Not enough aligned data yet.") From b515b0d095bcc8a5ed53a8a328b309dd0f6bd690 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Sun, 13 Apr 2025 14:34:02 +0200 Subject: [PATCH 10/18] data_map access --- src/data/accel/hbk/accelerometer.py | 77 ++++++++++++++++++-- src/data/accel/hbk/aligner.py | 109 ++++++++++++++-------------- tests/data/sources/test_mqtt.py | 54 +++++++++++++- 3 files changed, 179 insertions(+), 61 deletions(-) diff --git a/src/data/accel/hbk/accelerometer.py b/src/data/accel/hbk/accelerometer.py index c243db9..5080900 100644 --- a/src/data/accel/hbk/accelerometer.py +++ b/src/data/accel/hbk/accelerometer.py @@ -1,7 +1,9 @@ import threading import struct from collections import deque +from typing import Tuple, Any, Optional, List import numpy as np +import paho.mqtt.client as mqtt # Project Imports from data.accel.accelerometer import IAccelerometer @@ -12,7 +14,7 @@ class Accelerometer(IAccelerometer): def __init__( self, - mqtt_client, + mqtt_client: mqtt.Client, topic: str = "cpsens/d8-3a-dd-f5-92-48/cpsns_Simulator/1/acc/raw/data", map_size: int = MAX_MAP_SIZE ): @@ -35,7 +37,8 @@ def __init__( # Setting up MQTT callback self.mqtt_client.on_message = self._on_message - def _on_message(self, _, __, msg): + # pylint: disable=unused-argument + def _on_message(self, client: Any, userdata: Any, msg: mqtt.MQTTMessage) -> None: """Handles incoming MQTT messages.""" print(f"Received message on topic {msg.topic}") @@ -48,7 +51,7 @@ def safe_process(): # This ensures that an exception does not crash the entire threading.Thread(target=safe_process, daemon=True).start() - def process_message(self, msg): + def process_message(self, msg: mqtt.MQTTMessage) -> None: """ Processes incoming MQTT messages, extracts accelerometer data, and stores it in a dictionary of FIFO queues. @@ -91,7 +94,71 @@ def process_message(self, msg): print(f"Error processing message: {e}") - def read(self, requested_samples: int) -> (int, np.ndarray): + + def get_batch_size(self) -> Optional[int]: + """ + Returns the number of samples in the first available data batch. + Useful for determining alignment batch size. + """ + with self._lock: + if not self.data_map: + return None + first_key = next(iter(self.data_map)) + return len(self.data_map[first_key]) + + def get_sorted_keys(self) -> List[int]: + """ + Returns the sorted list of sample keys currently available. + """ + with self._lock: + return sorted(self.data_map.keys()) + + + def get_samples_for_key(self, key: int) -> Optional[List[float]]: + """ + Returns a copy of the sample list for a given key, + or None if the key is not present. + """ + with self._lock: + if key in self.data_map: + return list(self.data_map[key]) + return None + + def clear_used_data(self, start_key: int, samples_to_remove: int) -> None: + """ + Deletes all keys older than `start_key` and consumes `samples_to_remove` + samples starting from `start_key`, across subsequent keys in order. + """ + with self._lock: + # Delete older keys + keys_to_delete = [k for k in self.data_map if k < start_key] + for k in keys_to_delete: + del self.data_map[k] + + # Remove samples from start_key and onwards until all samples used are removed + keys = sorted(k for k in self.data_map if k >= start_key) + remaining_to_remove = samples_to_remove + + for key in keys: + if remaining_to_remove <= 0: + break + dq = self.data_map[key] + num_available = len(dq) + num_to_remove = min(remaining_to_remove, num_available) + + for _ in range(num_to_remove): + dq.popleft() + + if not dq: + del self.data_map[key] + + remaining_to_remove -= num_to_remove + + + + + + def read(self, requested_samples: int) -> Tuple[(int, np.ndarray)]: """ Reads the oldest accelerometer data from the FIFO buffer and removes only the read samples. @@ -134,5 +201,5 @@ def read(self, requested_samples: int) -> (int, np.ndarray): return status, samples - def acquire_lock(self)->(threading.Lock): + def acquire_lock(self)-> threading.Lock: return self._lock diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index 86f0166..56d2997 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -1,6 +1,8 @@ import threading +from typing import List, Tuple, Optional import numpy as np + #project imports from data.accel.hbk.accelerometer import Accelerometer # type: ignore @@ -25,42 +27,41 @@ def __init__(self, mqtt_client, topics: list, map_size=44840, missing_value=np.n self._lock = threading.Lock() seen = set() # Create one Accelerometer per uniqe topic - for topic in topics: - if topic not in seen: - seen.add(topic) - acc = Accelerometer(mqtt_client, topic=topic, map_size=map_size) - self.channels.append(acc) - mqtt_client.subscribe(topic, qos=1) - mqtt_client.message_callback_add(topic, lambda _, __, - msg, acc=acc: acc.process_message(msg)) + unique_topics = [topic for topic in topics if not (topic in seen or seen.add(topic))] + for topic in unique_topics: + seen.add(topic) + acc = Accelerometer(mqtt_client, topic=topic, map_size=map_size) + self.channels.append(acc) + mqtt_client.subscribe(topic, qos=1) + mqtt_client.message_callback_add(topic, lambda _, __, + msg, acc=acc: acc.process_message(msg)) - def find_continuous_key_groups(self): + def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[int]]]]: """ Determines the batch size, finds common keys, and groups them into continuous sequences. Returns: tuple: (batch_size, grouped_keys) or (None, None) if data is insufficient. - example of grouped keys: [[96, 128, 160, 192, 224, 256, 288, 320, 352, 384]] """ if not self.channels: return None, None - # Step 1: Determine batch size (By using the length of data samples in first messages, - # so all messages should contain the same number of data samples) + # Get the batch size from any channel batch_size = None for ch in self.channels: - if ch.data_map: - first_key = next(iter(ch.data_map)) - batch_size = len(ch.data_map[first_key]) + batch_size = ch.get_batch_size() + if batch_size is not None: break if batch_size is None: return None, None - # Step 2: Find common keys across channels - key_sets = [set(ch.data_map.keys()) for ch in self.channels] + # Get common keys across all channels + key_sets = [set(ch.get_sorted_keys()) for ch in self.channels] + if not key_sets: + return None, None common_keys = sorted(set.intersection(*key_sets)) - # Step 3: Group keys into continuous sequences + # Group keys into continuous sequences key_groups = [] current_group = [] @@ -77,62 +78,60 @@ def find_continuous_key_groups(self): return batch_size, key_groups - def extract(self, requested_samples: int) -> np.ndarray: """ Extracts a specified number of aligned samples from all channels. This method: 1. Uses `find_continuous_key_groups()` to determine batch size - and group keys into continuous aligned blocks. - 2. Searches for the first key group that contains enough samples. - 3. Collects aligned samples across all channels. - 4. Cleans up old and used data from each channel's buffer. + and group keys into continuous aligned blocks. + 2. Selects the first group that has enough samples. + 3. Collects aligned samples across all channels using their accessors. + 4. Cleans up used and older data via `clear_used_data()` on each Accelerometer. Parameters: requested_samples (int): The total number of samples to extract across all channels. Returns: np.ndarray: A 2D NumPy array of shape - (channels, requested_samples) containing aligned data. + (channels, requested_samples) containing aligned data. Returns an empty array if alignment is not possible. """ with self._lock: batch_size, key_groups = self.find_continuous_key_groups() - print("Keys",key_groups) + print("Keys", key_groups) + if batch_size is None or not key_groups: return np.empty((0, len(self.channels)), dtype=np.float32) - # Pick the first group that gives us enough samples for group in key_groups: total_samples = len(group) * batch_size - if total_samples >= requested_samples: - aligned_data = [[] for _ in self.channels] - samples_collected = 0 - - for key in group: - entries = [list(ch.data_map[key]) for ch in self.channels] - for i in range(batch_size): - if samples_collected >= requested_samples: - break - for ch_idx, channel_data in enumerate(entries): - aligned_data[ch_idx].append(channel_data[i]) - samples_collected += 1 - - # Delete used and older data - for ch in self.channels: - for k in list(ch.data_map.keys()): - if k < group[0]: - del ch.data_map[k] - elif k in group: - for _ in range(min(requested_samples, len(ch.data_map[k]))): - ch.data_map[k].popleft() - if not ch.data_map[k]: - del ch.data_map[k] - - aligned_array = np.array(aligned_data, dtype=np.float32) - print(f"Aligned shape: {aligned_array.shape}") - return aligned_array - - # No group had enough samples + if total_samples < requested_samples: + continue # Skip groups that don't have enough samples + + # Proceed with aligned extraction + aligned_data = [[] for _ in self.channels] + samples_collected = 0 + + for key in group: + entries = [ch.get_samples_for_key(key) for ch in self.channels] + + for i in range(batch_size): + if samples_collected >= requested_samples: + break + for ch_idx, channel_data in enumerate(entries): + aligned_data[ch_idx].append(channel_data[i]) + samples_collected += 1 + + if samples_collected >= requested_samples: + break + + # Clean up used and older data + for ch in self.channels: + ch.clear_used_data(group[0], requested_samples) + + aligned_array = np.array(aligned_data, dtype=np.float32) + print(f"Aligned shape: {aligned_array.shape}") + return aligned_array + return np.empty((0, len(self.channels)), dtype=np.float32) diff --git a/tests/data/sources/test_mqtt.py b/tests/data/sources/test_mqtt.py index 6779de8..b6dc1dd 100644 --- a/tests/data/sources/test_mqtt.py +++ b/tests/data/sources/test_mqtt.py @@ -1,15 +1,67 @@ import io import os +import json import pytest from unittest.mock import MagicMock + +from data.sources import mqtt from data.sources.mqtt import ( create_on_connect_callback, create_on_subscribe_callback, create_on_message_callback, create_on_publish_callback, - setup_mqtt_client + setup_mqtt_client, + load_config ) +def test_load_config_success(tmp_path): + config_data = {"key": "value"} + config_file = tmp_path / "config.json" + config_file.write_text(json.dumps(config_data), encoding="utf-8") + + loaded = load_config(str(config_file)) + assert loaded == config_data + + +def test_load_config_file_not_found(): + with pytest.raises(FileNotFoundError): + load_config("non_existing_config.json") + + + +def test_load_config_invalid_json(tmp_path): + invalid_file = tmp_path / "bad_config.json" + invalid_file.write_text("{invalid_json: True", encoding="utf-8") + with pytest.raises(ValueError): + load_config(str(invalid_file)) + + +def test_load_config_unexpected_exception(monkeypatch): + + def bad_open(*args, **kwargs): + raise OSError("Unexpected OS error") + + monkeypatch.setattr("builtins.open", bad_open) + + with pytest.raises(RuntimeError): + mqtt.load_config("config.json") + + +def test_setup_mqtt_client_invalid_index(): + dummy_config = { + "ClientID": "test_client", + "userId": "test_user", + "password": "test_pass", + "TopicsToSubscribe": ["topic1"], + "QoS": 1, + "host": "localhost", + "port": 1883 + } + + with pytest.raises(ValueError): + setup_mqtt_client(dummy_config, topic_index=5) + + def test_on_connect_callback_success(): topics = ["test/topic1", "test/topic2"] From 92ca1f91ec29cb79236949c9ef1f110bd2fb050b Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Sun, 13 Apr 2025 20:34:22 +0200 Subject: [PATCH 11/18] changed test directory --- tests/{ => integration}/data/accel/hbk/constants.py | 0 .../data/accel/hbk/test_accelerometer.py | 0 tests/{ => integration}/data/accel/hbk/test_aligner.py | 10 ---------- tests/{ => integration}/data/sources/test_mqtt.py | 0 4 files changed, 10 deletions(-) rename tests/{ => integration}/data/accel/hbk/constants.py (100%) rename tests/{ => integration}/data/accel/hbk/test_accelerometer.py (100%) rename tests/{ => integration}/data/accel/hbk/test_aligner.py (99%) rename tests/{ => integration}/data/sources/test_mqtt.py (100%) diff --git a/tests/data/accel/hbk/constants.py b/tests/integration/data/accel/hbk/constants.py similarity index 100% rename from tests/data/accel/hbk/constants.py rename to tests/integration/data/accel/hbk/constants.py diff --git a/tests/data/accel/hbk/test_accelerometer.py b/tests/integration/data/accel/hbk/test_accelerometer.py similarity index 100% rename from tests/data/accel/hbk/test_accelerometer.py rename to tests/integration/data/accel/hbk/test_accelerometer.py diff --git a/tests/data/accel/hbk/test_aligner.py b/tests/integration/data/accel/hbk/test_aligner.py similarity index 99% rename from tests/data/accel/hbk/test_aligner.py rename to tests/integration/data/accel/hbk/test_aligner.py index 931222c..ed5effe 100644 --- a/tests/data/accel/hbk/test_aligner.py +++ b/tests/integration/data/accel/hbk/test_aligner.py @@ -76,13 +76,6 @@ def publish_samples(client, topic, values: np.ndarray, start_key: int): print(f"[PUBLISH DEBUG] Topic: {topic}, Start key: {start_key}, Batch size: {len(batch_values)}") - - - - - - - def test_aligner_continuous_block_required(mqtt_setup): client, topics = mqtt_setup aligner = Aligner(client, topics=topics, map_size=512) @@ -105,9 +98,6 @@ def test_aligner_continuous_block_required(mqtt_setup): assert np.allclose(aligned[2, :5], np.arange(5)), "Check data from channel 3" -# TODO: Check specifc data - - def test_aligner_extract_removes_used_and_older_data(mqtt_setup): diff --git a/tests/data/sources/test_mqtt.py b/tests/integration/data/sources/test_mqtt.py similarity index 100% rename from tests/data/sources/test_mqtt.py rename to tests/integration/data/sources/test_mqtt.py From c183ff1b21a1d6e71cf338d29cb1364ec4112de6 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Sun, 13 Apr 2025 20:36:19 +0200 Subject: [PATCH 12/18] minor change to aligner --- src/data/accel/hbk/aligner.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index 56d2997..b88eed7 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -52,12 +52,10 @@ def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[ batch_size = ch.get_batch_size() if batch_size is not None: break - if batch_size is None: - return None, None # Get common keys across all channels key_sets = [set(ch.get_sorted_keys()) for ch in self.channels] - if not key_sets: + if not key_sets or batch_size is None: return None, None common_keys = sorted(set.intersection(*key_sets)) @@ -101,21 +99,16 @@ def extract(self, requested_samples: int) -> np.ndarray: batch_size, key_groups = self.find_continuous_key_groups() print("Keys", key_groups) - if batch_size is None or not key_groups: - return np.empty((0, len(self.channels)), dtype=np.float32) - for group in key_groups: total_samples = len(group) * batch_size if total_samples < requested_samples: continue # Skip groups that don't have enough samples - # Proceed with aligned extraction aligned_data = [[] for _ in self.channels] samples_collected = 0 for key in group: entries = [ch.get_samples_for_key(key) for ch in self.channels] - for i in range(batch_size): if samples_collected >= requested_samples: break From 60cbeccfc5393c44abec6479e7fc325f1fce9087 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Mon, 14 Apr 2025 12:53:30 +0200 Subject: [PATCH 13/18] unit_tests --- src/data/accel/hbk/aligner.py | 3 + .../data/accel/hbk/test_accelerometer_unit.py | 198 ++++++++++++++++++ .../unit/data/accel/hbk/test_aligner_unit.py | 120 +++++++++++ 3 files changed, 321 insertions(+) create mode 100644 tests/unit/data/accel/hbk/test_accelerometer_unit.py create mode 100644 tests/unit/data/accel/hbk/test_aligner_unit.py diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index b88eed7..707b1b5 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -99,6 +99,9 @@ def extract(self, requested_samples: int) -> np.ndarray: batch_size, key_groups = self.find_continuous_key_groups() print("Keys", key_groups) + if batch_size is None or key_groups is None: + return np.empty((0, len(self.channels)), dtype=np.float32) + for group in key_groups: total_samples = len(group) * batch_size if total_samples < requested_samples: diff --git a/tests/unit/data/accel/hbk/test_accelerometer_unit.py b/tests/unit/data/accel/hbk/test_accelerometer_unit.py new file mode 100644 index 0000000..1bc2bba --- /dev/null +++ b/tests/unit/data/accel/hbk/test_accelerometer_unit.py @@ -0,0 +1,198 @@ +import struct +import threading +import pytest +import numpy as np +from unittest.mock import MagicMock +from data.accel.hbk.accelerometer import Accelerometer +from data.accel.metadata_constants import DESCRIPTOR_LENGTH_BYTES + + + +@pytest.fixture +def mock_mqtt_client(): + return MagicMock() + + +@pytest.fixture +def test_accelerometer(mock_mqtt_client): + return Accelerometer(mock_mqtt_client, topic="test/topic", map_size=128) + + +class MockMQTTMessage: + def __init__(self, topic, payload): + self.topic = topic + self.payload = payload + + +def make_mock_payload(start_key: int, num_samples: int = 32) -> bytes: + descriptor_length = 28 + descriptor = struct.pack(" Date: Mon, 14 Apr 2025 16:04:20 +0200 Subject: [PATCH 14/18] aligner now also returns UTC. --- src/data/accel/hbk/aligner.py | 12 ++++++++---- src/examples/experiment_2.py | 3 ++- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index 707b1b5..1c8d875 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -1,5 +1,6 @@ import threading from typing import List, Tuple, Optional +from datetime import datetime, timedelta import numpy as np @@ -91,9 +92,10 @@ def extract(self, requested_samples: int) -> np.ndarray: requested_samples (int): The total number of samples to extract across all channels. Returns: - np.ndarray: A 2D NumPy array of shape - (channels, requested_samples) containing aligned data. - Returns an empty array if alignment is not possible. + tuple: (aligned_data, utc_timestamp) + aligned_data is a NumPy array of shape (channels, requested_samples) + utc_timestamp is the UTC time of the first aligned sample. + Returns an empty array if alignment is not possible. """ with self._lock: batch_size, key_groups = self.find_continuous_key_groups() @@ -109,6 +111,8 @@ def extract(self, requested_samples: int) -> np.ndarray: # Proceed with aligned extraction aligned_data = [[] for _ in self.channels] samples_collected = 0 + utc_time = datetime.utcnow() + for key in group: entries = [ch.get_samples_for_key(key) for ch in self.channels] @@ -128,6 +132,6 @@ def extract(self, requested_samples: int) -> np.ndarray: aligned_array = np.array(aligned_data, dtype=np.float32) print(f"Aligned shape: {aligned_array.shape}") - return aligned_array + return aligned_array, utc_time return np.empty((0, len(self.channels)), dtype=np.float32) diff --git a/src/examples/experiment_2.py b/src/examples/experiment_2.py index fea6689..2931691 100644 --- a/src/examples/experiment_2.py +++ b/src/examples/experiment_2.py @@ -26,10 +26,11 @@ def main(): while True: time.sleep(1) - data = aligner.extract(16) + data, Utime = aligner.extract(16) if data.shape[0] == 0: print("Not enough aligned data yet.") else: + print(f"Colllected this batch at:{Utime}") print(f"Extracted aligned data shape: {data.shape}\n{data}") break time.sleep(1) From 1e8544e78f6b7f7ab6b9a191ae12122fc0f2ee1a Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Mon, 14 Apr 2025 22:13:24 +0200 Subject: [PATCH 15/18] small bug --- tests/integration/data/accel/hbk/test_aligner.py | 6 +++--- tests/unit/data/accel/hbk/test_aligner_unit.py | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/integration/data/accel/hbk/test_aligner.py b/tests/integration/data/accel/hbk/test_aligner.py index ed5effe..fbeb8ca 100644 --- a/tests/integration/data/accel/hbk/test_aligner.py +++ b/tests/integration/data/accel/hbk/test_aligner.py @@ -91,7 +91,7 @@ def test_aligner_continuous_block_required(mqtt_setup): time.sleep(1.5) # Let messages arrive - aligned = aligner.extract(128) # Should use keys 96, 128, 160, 192 (128 samples) + aligned, _ = aligner.extract(128) # Should use keys 96, 128, 160, 192 (128 samples) assert aligned.shape == (3, 128), f"Expected 128 aligned rows, got {aligned.shape}" assert np.allclose(aligned[0, :5], np.arange(5)), "Check data from channel 1" @@ -112,7 +112,7 @@ def test_aligner_extract_removes_used_and_older_data(mqtt_setup): time.sleep(1) # Extract 96 samples → should consume keys 0, 32, 64 (96 samples) - aligned = aligner.extract(96) + aligned, _ = aligner.extract(96) assert aligned.shape == (3, 96), "Expected 96 aligned samples" @@ -139,7 +139,7 @@ def test_aligner_single_channel_extract_and_cleanup(mqtt_setup): time.sleep(1) # Extract 64 samples from the single channel - extracted = aligner.extract(64) + extracted, _ = aligner.extract(64) assert extracted.shape == (1, 64), f"Expected shape (64, 1), got {extracted.shape}" assert np.allclose(extracted.flatten()[:5], [0, 1, 2, 3, 4]), "Unexpected values in extracted data" diff --git a/tests/unit/data/accel/hbk/test_aligner_unit.py b/tests/unit/data/accel/hbk/test_aligner_unit.py index 5881eaf..e3f69af 100644 --- a/tests/unit/data/accel/hbk/test_aligner_unit.py +++ b/tests/unit/data/accel/hbk/test_aligner_unit.py @@ -37,7 +37,7 @@ def test_find_continuous_key_groups(aligner_with_mock_channels): def test_extract_with_enough_samples(aligner_with_mock_channels): aligner, accelerometers = aligner_with_mock_channels - result = aligner.extract(8) + result, _ = aligner.extract(8) assert result.shape == (3, 8) expected = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0] @@ -50,7 +50,7 @@ def test_extract_with_enough_samples(aligner_with_mock_channels): def test_extract_too_few_samples_returns_empty(aligner_with_mock_channels): aligner, _ = aligner_with_mock_channels - result = aligner.extract(200) # more than available + result = aligner.extract(210) # more than available it should return empty array, no timestamp assert result.shape == (0, 3) @@ -107,7 +107,7 @@ def test_extract_skips_initial_and_gaps_until_valid_block(aligner_with_mock_chan acc.get_samples_for_key.side_effect = lambda key: [float(key + i) for i in range(batch_size)] # Extract 128 samples - result = aligner.extract(required_samples) + result, _ = aligner.extract(required_samples) # Assert correct shape assert result.shape == (3, 128), f"Expected (3, 128), got {result.shape}" From 698494b90d0fa893ca5fbaa1ff890555948b83ee Mon Sep 17 00:00:00 2001 From: prasadtalasila Date: Mon, 14 Apr 2025 22:36:18 +0200 Subject: [PATCH 16/18] minor fixes --- poetry.lock | 20 +++++++++++++++++++- pyproject.toml | 1 + src/data/accel/accelerometer.py | 1 - src/data/accel/hbk/accelerometer.py | 6 ++---- src/data/accel/hbk/aligner.py | 7 +++---- src/data/accel/random.py | 28 ---------------------------- src/examples/experiment_2.py | 4 ++-- 7 files changed, 27 insertions(+), 40 deletions(-) delete mode 100644 src/data/accel/random.py diff --git a/poetry.lock b/poetry.lock index 4286811..cdd770a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -347,6 +347,24 @@ pytest = ">=4.6" [package.extras] testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] +[[package]] +name = "pytest-mock" +version = "3.14.0" +description = "Thin-wrapper around the mock package for easier use with pytest" +optional = false +python-versions = ">=3.8" +groups = ["dev"] +files = [ + {file = "pytest-mock-3.14.0.tar.gz", hash = "sha256:2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0"}, + {file = "pytest_mock-3.14.0-py3-none-any.whl", hash = "sha256:0b72c38033392a5f4621342fe11e9219ac11ec9d375f8e2a0c164539e0d70f6f"}, +] + +[package.dependencies] +pytest = ">=6.2.5" + +[package.extras] +dev = ["pre-commit", "pytest-asyncio", "tox"] + [[package]] name = "tomlkit" version = "0.13.2" @@ -362,4 +380,4 @@ files = [ [metadata] lock-version = "2.1" python-versions = ">=3.12, <3.13" -content-hash = "8cf0e37ad4078f644257790a6604931972ec7ecf92f1eb369a516bd1721fd21c" +content-hash = "5be5e4e13be93614c6a8f1d722748f3ac25a3c50e59bb8366cdab3312d70e45e" diff --git a/pyproject.toml b/pyproject.toml index 9d192a8..e8d6d60 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ numpy = "^2.2.4" pylint = "^3.3.6" pytest = "^8.3.5" pytest-cov = "^6.1.1" +pytest-mock = "^3.14.0" [build-system] requires = ["poetry-core"] diff --git a/src/data/accel/accelerometer.py b/src/data/accel/accelerometer.py index a48a3fa..6dd890a 100644 --- a/src/data/accel/accelerometer.py +++ b/src/data/accel/accelerometer.py @@ -19,4 +19,3 @@ def read(self, requested_samples: int) -> (int, np.ndarray): # type: ignore } } """ - pass diff --git a/src/data/accel/hbk/accelerometer.py b/src/data/accel/hbk/accelerometer.py index 5080900..1cdead0 100644 --- a/src/data/accel/hbk/accelerometer.py +++ b/src/data/accel/hbk/accelerometer.py @@ -94,7 +94,6 @@ def process_message(self, msg: mqtt.MQTTMessage) -> None: print(f"Error processing message: {e}") - def get_batch_size(self) -> Optional[int]: """ Returns the number of samples in the first available data batch. @@ -106,6 +105,7 @@ def get_batch_size(self) -> Optional[int]: first_key = next(iter(self.data_map)) return len(self.data_map[first_key]) + def get_sorted_keys(self) -> List[int]: """ Returns the sorted list of sample keys currently available. @@ -124,6 +124,7 @@ def get_samples_for_key(self, key: int) -> Optional[List[float]]: return list(self.data_map[key]) return None + def clear_used_data(self, start_key: int, samples_to_remove: int) -> None: """ Deletes all keys older than `start_key` and consumes `samples_to_remove` @@ -155,9 +156,6 @@ def clear_used_data(self, start_key: int, samples_to_remove: int) -> None: remaining_to_remove -= num_to_remove - - - def read(self, requested_samples: int) -> Tuple[(int, np.ndarray)]: """ Reads the oldest accelerometer data from the FIFO buffer and removes only the read samples. diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index 1c8d875..a9bde2c 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -1,11 +1,10 @@ import threading from typing import List, Tuple, Optional -from datetime import datetime, timedelta +from datetime import datetime import numpy as np - #project imports -from data.accel.hbk.accelerometer import Accelerometer # type: ignore +from data.accel.hbk.accelerometer import Accelerometer class Aligner: @@ -103,7 +102,7 @@ def extract(self, requested_samples: int) -> np.ndarray: if batch_size is None or key_groups is None: return np.empty((0, len(self.channels)), dtype=np.float32) - + for group in key_groups: total_samples = len(group) * batch_size if total_samples < requested_samples: diff --git a/src/data/accel/random.py b/src/data/accel/random.py deleted file mode 100644 index de13600..0000000 --- a/src/data/accel/random.py +++ /dev/null @@ -1,28 +0,0 @@ -from datetime import datetime -import random -from .accelerometer import IAccelerometer, US_MULTIPLIER - -""" -A dummy accelerometer that generates -random (x,y,z) values in the [-1,1] range -""" - - -class RandomSource(IAccelerometer): - - def read(self) -> dict: - accel = { - 'x': random.uniform(-1, 1), - 'y': random.uniform(-1, 1), - 'z': random.uniform(-1, 1) - } - # represents time at resolution of a microsecond - # but depends on the underlying clock - timestamp = datetime.timestamp(datetime.now()) - # pylint: disable=unused-variable - key = round(timestamp * US_MULTIPLIER) - sample = { - 'timestamp': timestamp, - 'acceleration': accel - } - return sample diff --git a/src/examples/experiment_2.py b/src/examples/experiment_2.py index 2931691..73bb233 100644 --- a/src/examples/experiment_2.py +++ b/src/examples/experiment_2.py @@ -26,11 +26,11 @@ def main(): while True: time.sleep(1) - data, Utime = aligner.extract(16) + data, utime = aligner.extract(16) if data.shape[0] == 0: print("Not enough aligned data yet.") else: - print(f"Colllected this batch at:{Utime}") + print(f"Colllected this batch at:{utime}") print(f"Extracted aligned data shape: {data.shape}\n{data}") break time.sleep(1) From d5c2b596c1c7793219fa2f90f1c0852f2610d599 Mon Sep 17 00:00:00 2001 From: 8ohamed <114395272+8ohamed@users.noreply.github.com> Date: Tue, 15 Apr 2025 01:53:48 +0200 Subject: [PATCH 17/18] Class Interface + Fixed bugs in test --- pytest.ini | 7 + src/data/accel/accelerometer.py | 76 ++++++++-- src/data/accel/aligner.py | 36 +++++ src/data/accel/hbk/accelerometer.py | 4 - src/data/accel/hbk/aligner.py | 137 +++++++++--------- src/examples/experiment_1.py | 4 +- .../data/accel/hbk/test_accelerometer.py | 20 ++- .../data/accel/hbk/test_aligner.py | 15 +- tests/integration/data/sources/test_mqtt.py | 9 +- .../data/accel/hbk/test_accelerometer_unit.py | 16 +- .../unit/data/accel/hbk/test_aligner_unit.py | 6 +- 11 files changed, 202 insertions(+), 128 deletions(-) create mode 100644 src/data/accel/aligner.py diff --git a/pytest.ini b/pytest.ini index 4cb9017..e2d7a4a 100644 --- a/pytest.ini +++ b/pytest.ini @@ -13,3 +13,10 @@ log_date_format = %Y-%m-%d %H:%M:%S #timeout slow tests timeout=5 + +env = + MQTT_CONNECT_DELAY=0.5 + +markers = + unit: marks unit tests + integration: marks integration tests diff --git a/src/data/accel/accelerometer.py b/src/data/accel/accelerometer.py index 6dd890a..f8bf4a5 100644 --- a/src/data/accel/accelerometer.py +++ b/src/data/accel/accelerometer.py @@ -1,21 +1,69 @@ +# pylint: disable=W0107 import abc +from typing import Tuple, Optional, List import numpy as np -US_MULTIPLIER = 1000000 # factor to convert time to microseconds +class IAccelerometer(abc.ABC): + @abc.abstractmethod + def read(self, requested_samples: int) -> Tuple[int, np.ndarray]: + """ + Read and return the requested number of accelerometer samples from the buffer. + + Parameters: + requested_samples (int): The number of samples to retrieve. + + Returns: + Tuple[int, np.ndarray]: + - status: 1 if the requested number of samples was returned, + 0 if fewer samples were available. + - data: A NumPy array containing the retrieved samples. + """ + pass + + + @abc.abstractmethod + def get_batch_size(self) -> Optional[int]: + """ + Get the number of samples in the first data batch. + + Returns: + int or None: The size of the first batch, or None if no data is available. + """ + pass + + + @abc.abstractmethod + def get_sorted_keys(self) -> List[int]: + """ + Get the sorted list of keys (samples since data first acquisition) available in the buffer. + + Returns: + List[int]: Sorted keys representing batches of data. + """ + pass + + + @abc.abstractmethod + def get_samples_for_key(self, key: int) -> Optional[List[float]]: + """ + Get the list of samples for a given key. + + Parameters: + key (int): The identifier for the desired data batch. + + Returns: + List[float] or None: A copy of the sample list if the key exists, otherwise None. + """ + pass -class IAccelerometer(abc.ABC): @abc.abstractmethod - def read(self, requested_samples: int) -> (int, np.ndarray): # type: ignore - """ - This method provides a single accelerometer reading. - A sample reading is: - sample = { - 'timestamp': 0, - 'accel_readings': { - 'x': 0, - 'y': 0, - 'z': 0 - } - } + def clear_used_data(self, start_key: int, samples_to_remove: int) -> None: + """ + Remove old and used data from the buffer. + + Parameters: + start_key (int): The first key from which data will be retained. + samples_to_remove (int): The number of samples to remove starting from `start_key`. """ + pass diff --git a/src/data/accel/aligner.py b/src/data/accel/aligner.py new file mode 100644 index 0000000..e8d79f9 --- /dev/null +++ b/src/data/accel/aligner.py @@ -0,0 +1,36 @@ +# pylint: disable=W0107 +import abc +from datetime import datetime +from typing import List, Optional, Tuple +import numpy as np + +class IAligner(abc.ABC): + @abc.abstractmethod + def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[int]]]]: + """ + Finds common continuous key groups across all channels. + + Returns: + Tuple: + - batch_size (Optional[int]): Size of each data batch if found, else None. + - key_groups (Optional[List[List[int]]]): + Groups of continuous sample keys common to all channels. + """ + pass + + + @abc.abstractmethod + def extract(self, requested_samples: int) -> Tuple[np.ndarray, Optional[datetime]]: + """ + Extracts aligned accelerometer samples from all channels. + + Parameters: + requested_samples (int): The number of aligned samples to extract. + + Returns: + Tuple: + - np.ndarray: A 2D NumPy array of shape (num_channels, num_samples). + - Optional[datetime]: UTC timestamp + when the aligned samples were extracted, or None on failure. + """ + pass diff --git a/src/data/accel/hbk/accelerometer.py b/src/data/accel/hbk/accelerometer.py index 1cdead0..1df62ae 100644 --- a/src/data/accel/hbk/accelerometer.py +++ b/src/data/accel/hbk/accelerometer.py @@ -4,21 +4,17 @@ from typing import Tuple, Any, Optional, List import numpy as np import paho.mqtt.client as mqtt - # Project Imports from data.accel.accelerometer import IAccelerometer from data.accel.constants import MAX_MAP_SIZE from data.accel.metadata_constants import DESCRIPTOR_LENGTH_BYTES - class Accelerometer(IAccelerometer): def __init__( self, mqtt_client: mqtt.Client, topic: str = "cpsens/d8-3a-dd-f5-92-48/cpsns_Simulator/1/acc/raw/data", map_size: int = MAX_MAP_SIZE ): - - """ Initializes the Accelerometer instance with a pre-configured MQTT client. diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index a9bde2c..ce1b0d8 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -3,7 +3,7 @@ from datetime import datetime import numpy as np -#project imports +# project imports from data.accel.hbk.accelerometer import Accelerometer @@ -33,37 +33,34 @@ def __init__(self, mqtt_client, topics: list, map_size=44840, missing_value=np.n acc = Accelerometer(mqtt_client, topic=topic, map_size=map_size) self.channels.append(acc) mqtt_client.subscribe(topic, qos=1) - mqtt_client.message_callback_add(topic, lambda _, __, - msg, acc=acc: acc.process_message(msg)) + mqtt_client.message_callback_add(topic, lambda _, + __, msg, acc=acc: acc.process_message(msg)) - def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[int]]]]: + def _get_common_keys(self, batch_size: Optional[int]) -> Optional[List[int]]: """ - Determines the batch size, finds common keys, and groups them into continuous sequences. + Gets the sorted list of keys that are common across all channels. + Returns: - tuple: (batch_size, grouped_keys) or (None, None) if data is insufficient. + A sorted list of common keys or None if batch_size is invalid. """ - if not self.channels: - return None, None - - # Get the batch size from any channel - batch_size = None - for ch in self.channels: - batch_size = ch.get_batch_size() - if batch_size is not None: - break - # Get common keys across all channels key_sets = [set(ch.get_sorted_keys()) for ch in self.channels] if not key_sets or batch_size is None: - return None, None - common_keys = sorted(set.intersection(*key_sets)) + return None + return sorted(set.intersection(*key_sets)) + + + def _group_continuous_keys(self, keys: List[int], batch_size: int) -> List[List[int]]: + """ + Groups sorted keys into continuous sequences based on batch_size. - # Group keys into continuous sequences + Returns: + A list of key groups (each group is a list of consecutive keys). + """ key_groups = [] current_group = [] - - for key in common_keys: + for key in keys: if not current_group: current_group.append(key) elif key == current_group[-1] + batch_size: @@ -73,64 +70,70 @@ def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[ current_group = [key] if current_group: key_groups.append(current_group) + return key_groups - return batch_size, key_groups - def extract(self, requested_samples: int) -> np.ndarray: - """ - Extracts a specified number of aligned samples from all channels. + def find_continuous_key_groups(self) -> Tuple[Optional[int], Optional[List[List[int]]]]: + if not self.channels: + return None, None - This method: - 1. Uses `find_continuous_key_groups()` to determine batch size - and group keys into continuous aligned blocks. - 2. Selects the first group that has enough samples. - 3. Collects aligned samples across all channels using their accessors. - 4. Cleans up used and older data via `clear_used_data()` on each Accelerometer. + batch_size = None + for ch in self.channels: + batch_size = ch.get_batch_size() + if batch_size is not None: + break + common_keys = self._get_common_keys(batch_size) + if common_keys is None: + return None, None + return batch_size, self._group_continuous_keys(common_keys, batch_size) - Parameters: - requested_samples (int): The total number of samples to extract across all channels. + + def _extract_aligned_block(self, group: List[int], batch_size: int, + requested_samples: int) -> Tuple[np.ndarray, datetime]: + """ + Extracts samples from the given aligned key group. + + Collects aligned samples across all channels and returns them + along with the UTC timestamp of the first aligned sample. Returns: - tuple: (aligned_data, utc_timestamp) - aligned_data is a NumPy array of shape (channels, requested_samples) - utc_timestamp is the UTC time of the first aligned sample. - Returns an empty array if alignment is not possible. + A tuple (aligned_data, utc_time) """ + aligned_data = [[] for _ in self.channels] + samples_collected = 0 + utc_time = datetime.utcnow() + + for key in group: + entries = [ch.get_samples_for_key(key) for ch in self.channels] + for i in range(batch_size): + if samples_collected >= requested_samples: + break + for ch_idx, channel_data in enumerate(entries): + aligned_data[ch_idx].append(channel_data[i]) + samples_collected += 1 + if samples_collected >= requested_samples: + break + + for ch in self.channels: + ch.clear_used_data(group[0], requested_samples) + + aligned_array = np.array(aligned_data, dtype=np.float32) + print(f"Aligned shape: {aligned_array.shape}") + return aligned_array, utc_time + + + def extract(self, requested_samples: int) -> Tuple[np.ndarray, Optional[datetime]]: with self._lock: batch_size, key_groups = self.find_continuous_key_groups() print("Keys", key_groups) if batch_size is None or key_groups is None: - return np.empty((0, len(self.channels)), dtype=np.float32) + # No data or groups to align, returun empty + return np.empty((0, len(self.channels)), dtype=np.float32), None for group in key_groups: total_samples = len(group) * batch_size - if total_samples < requested_samples: - continue # Skip groups that don't have enough samples - # Proceed with aligned extraction - aligned_data = [[] for _ in self.channels] - samples_collected = 0 - utc_time = datetime.utcnow() - - - for key in group: - entries = [ch.get_samples_for_key(key) for ch in self.channels] - for i in range(batch_size): - if samples_collected >= requested_samples: - break - for ch_idx, channel_data in enumerate(entries): - aligned_data[ch_idx].append(channel_data[i]) - samples_collected += 1 - - if samples_collected >= requested_samples: - break - - # Clean up used and older data - for ch in self.channels: - ch.clear_used_data(group[0], requested_samples) - - aligned_array = np.array(aligned_data, dtype=np.float32) - print(f"Aligned shape: {aligned_array.shape}") - return aligned_array, utc_time - - return np.empty((0, len(self.channels)), dtype=np.float32) + if total_samples >= requested_samples: + return self._extract_aligned_block(group, batch_size, requested_samples) + # No data or groups to align, returun empty + return np.empty((0, len(self.channels)), dtype=np.float32), None diff --git a/src/examples/experiment_1.py b/src/examples/experiment_1.py index 0fe1c99..2478b0a 100644 --- a/src/examples/experiment_1.py +++ b/src/examples/experiment_1.py @@ -25,7 +25,7 @@ def main(): with accelerometer.acquire_lock(): accelerometer.data_map.clear() - time.sleep(10) # Allow time for data collection + time.sleep(1) # Allow time for data collection with accelerometer.acquire_lock(): # This print to see the dictionary for key, fifo in sorted(accelerometer.data_map.items()): @@ -35,6 +35,8 @@ def main(): mqtt_client.loop_stop() mqtt_client.disconnect() + time.sleep(1) + print("Exiting cleanly") if __name__ == '__main__': main() diff --git a/tests/integration/data/accel/hbk/test_accelerometer.py b/tests/integration/data/accel/hbk/test_accelerometer.py index 6f3d05b..795b3bf 100644 --- a/tests/integration/data/accel/hbk/test_accelerometer.py +++ b/tests/integration/data/accel/hbk/test_accelerometer.py @@ -2,12 +2,14 @@ import json import pytest import struct +import os import numpy as np from data.accel.hbk.accelerometer import Accelerometer # type: ignore from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE from data.sources.mqtt import setup_mqtt_client, load_config import uuid +pytestmark = pytest.mark.integration @pytest.fixture(scope="function") @@ -21,7 +23,8 @@ def mqtt_client(): client.connect(mqtt_config["host"], mqtt_config["port"], 60) client.loop_start() - time.sleep(0.5) + connect_delay = float(os.environ.get("MQTT_CONNECT_DELAY")) + time.sleep(connect_delay) yield client, selected_topic client.loop_stop() @@ -60,8 +63,6 @@ def publish_binary_samples(client, topic, start, end): result.wait_for_publish() - - def test_accelerometer_read_in_steps(client_and_topic, accelerometer_instance): """ Test that reading in steps correctly retrieves the oldest samples @@ -113,18 +114,18 @@ def test_accelerometer_read_full_fifo(client_and_topic, accelerometer_instance): """ client, topic = client_and_topic - publish_binary_samples(client, topic, 0, 96) + publish_binary_samples(client, topic, 0, 64) total_samples = 0 while total_samples < 60: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) - status, data = accelerometer_instance.read(96) + status, data = accelerometer_instance.read(64) assert status == 1, f"Expected status 1, but got {status}" - assert data.shape == (96,), f"Unexpected shape: {data.shape}" - assert np.allclose(data, np.arange(96)), f"Order mismatch: {data[:10]}" + assert data.shape == (64,), f"Unexpected shape: {data.shape}" + assert np.allclose(data, np.arange(64)), f"Order mismatch: {data[:10]}" def test_accelerometer_read_partial_fifo(client_and_topic, accelerometer_instance): @@ -144,7 +145,7 @@ def test_accelerometer_read_partial_fifo(client_and_topic, accelerometer_instanc publish_binary_samples(client, topic, 0, 64) total_samples = 0 - while total_samples < 60: + while total_samples < 33: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) @@ -226,14 +227,11 @@ def test_accelerometer_reordering_late_sample(client_and_topic, accelerometer_in # Publish middle batch (32–63) AFTER last batch publish_binary_samples(client, topic, 32, 64) - total_samples = 0 while total_samples < 60: with accelerometer_instance._lock: total_samples = sum(len(deque) for deque in accelerometer_instance.data_map.values()) status, data = accelerometer_instance.read(96) - - assert status == 1, f"Expected status 1, but got {status}" assert data.shape == (96,), f"Unexpected shape: {data.shape}" expected_data = np.arange(96) # Expected: 0, 1, 2, ..., 95 diff --git a/tests/integration/data/accel/hbk/test_aligner.py b/tests/integration/data/accel/hbk/test_aligner.py index fbeb8ca..d446e99 100644 --- a/tests/integration/data/accel/hbk/test_aligner.py +++ b/tests/integration/data/accel/hbk/test_aligner.py @@ -1,17 +1,17 @@ import time import json +import os import pytest import struct - import numpy as np -from data.accel.hbk.aligner import Aligner # type: ignore - +from data.accel.hbk.aligner import Aligner # type: ignore from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE from data.sources.mqtt import setup_mqtt_client, load_config import uuid - +pytestmark = pytest.mark.integration +connect_delay = float(os.environ.get("MQTT_CONNECT_DELAY")) @pytest.fixture(scope="function") def mqtt_client_and_config(): @@ -22,7 +22,7 @@ def mqtt_client_and_config(): client, _ = setup_mqtt_client(mqtt_config, topic_index=0) client.connect(mqtt_config["host"], mqtt_config["port"], 60) client.loop_start() - time.sleep(0.1) + time.sleep(connect_delay) yield client, mqtt_config @@ -40,7 +40,7 @@ def mqtt_setup(): client, _ = setup_mqtt_client(mqtt_config, 0) client.connect(mqtt_config["host"], mqtt_config["port"], 60) client.loop_start() - time.sleep(0.1) + time.sleep(connect_delay) # Extract topics manually topics = [ @@ -98,8 +98,6 @@ def test_aligner_continuous_block_required(mqtt_setup): assert np.allclose(aligned[2, :5], np.arange(5)), "Check data from channel 3" - - def test_aligner_extract_removes_used_and_older_data(mqtt_setup): client, topics = mqtt_setup aligner = Aligner(client, topics=topics, map_size=512) @@ -125,7 +123,6 @@ def test_aligner_extract_removes_used_and_older_data(mqtt_setup): f"Channel {i+1} still contains old data (keys <= 64): {remaining_keys}" - def test_aligner_single_channel_extract_and_cleanup(mqtt_setup): client, topics = mqtt_setup one_topic = [topics[0]] # Use only the first topic diff --git a/tests/integration/data/sources/test_mqtt.py b/tests/integration/data/sources/test_mqtt.py index b6dc1dd..7cef093 100644 --- a/tests/integration/data/sources/test_mqtt.py +++ b/tests/integration/data/sources/test_mqtt.py @@ -28,7 +28,6 @@ def test_load_config_file_not_found(): load_config("non_existing_config.json") - def test_load_config_invalid_json(tmp_path): invalid_file = tmp_path / "bad_config.json" invalid_file.write_text("{invalid_json: True", encoding="utf-8") @@ -62,7 +61,6 @@ def test_setup_mqtt_client_invalid_index(): setup_mqtt_client(dummy_config, topic_index=5) - def test_on_connect_callback_success(): topics = ["test/topic1", "test/topic2"] qos = 1 @@ -75,6 +73,7 @@ def test_on_connect_callback_success(): for topic in topics: client.subscribe.assert_any_call(topic, qos=qos) + def test_on_connect_callback_failure(): topics = ["test/topic1", "test/topic2"] qos = 1 @@ -85,6 +84,7 @@ def test_on_connect_callback_failure(): # Verify that subscribe is not called when connection fails. client.subscribe.assert_not_called() + def test_on_subscribe_callback(capsys): on_subscribe = create_on_subscribe_callback() client = MagicMock() @@ -94,6 +94,7 @@ def test_on_subscribe_callback(capsys): assert "Subscription ID 42" in captured assert "QoS levels [1, 1]" in captured + def test_on_message_callback(capsys): on_message = create_on_message_callback() client = MagicMock() @@ -109,6 +110,7 @@ class FakeMsg: assert "Received message on test/topic" in captured #assert "Message payload: test payload" in captured + def test_on_publish_callback(capsys): on_publish = create_on_publish_callback() client = MagicMock() @@ -127,7 +129,6 @@ def test_setup_mqtt_client(): "host": "localhost", "port": 1883 } - # Unpack the returned tuple client, selected_topic = setup_mqtt_client(dummy_config) @@ -141,5 +142,3 @@ def test_setup_mqtt_client(): assert client.on_message is not None assert client.on_publish is not None - # Optional: Ensure the correct topic is selected - assert selected_topic == "test/topic1" # Since topic_index defaults to 0 diff --git a/tests/unit/data/accel/hbk/test_accelerometer_unit.py b/tests/unit/data/accel/hbk/test_accelerometer_unit.py index 1bc2bba..a6c6f84 100644 --- a/tests/unit/data/accel/hbk/test_accelerometer_unit.py +++ b/tests/unit/data/accel/hbk/test_accelerometer_unit.py @@ -6,7 +6,7 @@ from data.accel.hbk.accelerometer import Accelerometer from data.accel.metadata_constants import DESCRIPTOR_LENGTH_BYTES - +pytestmark = pytest.mark.unit @pytest.fixture def mock_mqtt_client(): @@ -17,7 +17,6 @@ def mock_mqtt_client(): def test_accelerometer(mock_mqtt_client): return Accelerometer(mock_mqtt_client, topic="test/topic", map_size=128) - class MockMQTTMessage: def __init__(self, topic, payload): self.topic = topic @@ -53,9 +52,6 @@ def test_get_batch_size(test_accelerometer): assert batch_size == 32 - - - def test_clear_used_data_removes_samples_and_keys(test_accelerometer): # Add three batches: 0–31, 32–63, 64–95 for i in range(3): @@ -80,11 +76,6 @@ def test_clear_used_data_removes_samples_and_keys(test_accelerometer): assert remaining_samples == 14 - - - - - def test_read_fewer_than_available(test_accelerometer): for i in range(3): msg = MockMQTTMessage("test/topic", make_mock_payload(i * 32)) @@ -114,10 +105,6 @@ def test_get_batch_size_returns_none_when_empty(test_accelerometer): assert test_accelerometer.get_batch_size() is None - - - - def test_on_message_invokes_process_in_thread(test_accelerometer, mocker): msg = MockMQTTMessage("test/topic", make_mock_payload(0)) process_mock = mocker.patch.object(test_accelerometer, "process_message") @@ -186,7 +173,6 @@ def test_process_message_triggers_eviction_when_map_size_exceeded(): assert keys == [32, 64], f"Eviction did not occur correctly. Remaining keys: {keys}" - def test_clear_used_data_with_zero_samples_to_remove_does_nothing(test_accelerometer): # Add a single batch msg = MockMQTTMessage("test/topic", make_mock_payload(0)) diff --git a/tests/unit/data/accel/hbk/test_aligner_unit.py b/tests/unit/data/accel/hbk/test_aligner_unit.py index e3f69af..f41f754 100644 --- a/tests/unit/data/accel/hbk/test_aligner_unit.py +++ b/tests/unit/data/accel/hbk/test_aligner_unit.py @@ -2,6 +2,7 @@ import numpy as np from unittest.mock import MagicMock, patch from data.accel.hbk.aligner import Aligner # type: ignore +pytestmark = pytest.mark.unit @pytest.fixture @@ -50,7 +51,7 @@ def test_extract_with_enough_samples(aligner_with_mock_channels): def test_extract_too_few_samples_returns_empty(aligner_with_mock_channels): aligner, _ = aligner_with_mock_channels - result = aligner.extract(210) # more than available it should return empty array, no timestamp + result, _ = aligner.extract(210) # more than available it should return empty array, None assert result.shape == (0, 3) @@ -59,6 +60,7 @@ def test_find_continuous_key_groups_no_channels(): batch_size, key_groups = aligner.find_continuous_key_groups() assert batch_size is None and key_groups is None + def test_find_continuous_key_groups_handles_last_group(): aligner = Aligner(mqtt_client=MagicMock(), topics=["t1", "t2"]) @@ -73,6 +75,7 @@ def test_find_continuous_key_groups_handles_last_group(): batch_size, groups = aligner.find_continuous_key_groups() assert groups == [[0, 4, 8]] + def test_find_continuous_key_groups_returns_none_when_batch_size_none(): ch = MagicMock() ch.get_batch_size.return_value = None @@ -86,7 +89,6 @@ def test_find_continuous_key_groups_returns_none_when_batch_size_none(): assert key_groups is None - def test_extract_skips_initial_and_gaps_until_valid_block(aligner_with_mock_channels): aligner, accelerometers = aligner_with_mock_channels From c40506ffc13f0a4db58a3bf9468daa6231db547c Mon Sep 17 00:00:00 2001 From: prasadtalasila Date: Tue, 15 Apr 2025 17:15:31 +0200 Subject: [PATCH 18/18] Fixes minor errors and improves docs --- .coveragerc | 3 ++- README.md | 8 ++++++- poetry.lock | 22 +++++++++++++++++-- pyproject.toml | 1 + src/data/accel/hbk/aligner.py | 5 +++-- src/examples/README.md | 12 +++++++--- src/examples/experiment_1.py | 9 ++++---- src/examples/experiment_2.py | 4 ++-- .../data/accel/hbk/test_accelerometer.py | 2 +- .../data/accel/hbk/test_aligner.py | 2 +- .../unit/data/accel/hbk/test_aligner_unit.py | 2 +- 11 files changed, 52 insertions(+), 18 deletions(-) diff --git a/.coveragerc b/.coveragerc index e3ff08e..9ecf53f 100644 --- a/.coveragerc +++ b/.coveragerc @@ -4,7 +4,8 @@ omit = */venv/* */.venv/* */__init__.py - */src/data/accel/random.py + */src/data/accel/accelerometer.py + */src/data/accel/aligner.py */src/examples/* [report] diff --git a/README.md b/README.md index 747d170..2b638fd 100644 --- a/README.md +++ b/README.md @@ -32,5 +32,11 @@ Write tests in the _tests_ directory. Be sure to name any new files as _test_*_.py_. To run all tests, with coverage: ```bash -pytest +pytest -m unit # run unit tests +pytest -m integration # run integration tests +pytest # run all the tests ``` + +## Use + +Please see [examples](src/examples/README.md) for typical usage of the package. diff --git a/poetry.lock b/poetry.lock index cdd770a..5a2c117 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. [[package]] name = "astroid" @@ -347,6 +347,24 @@ pytest = ">=4.6" [package.extras] testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] +[[package]] +name = "pytest-env" +version = "1.1.5" +description = "pytest plugin that allows you to add environment variables." +optional = false +python-versions = ">=3.8" +groups = ["dev"] +files = [ + {file = "pytest_env-1.1.5-py3-none-any.whl", hash = "sha256:ce90cf8772878515c24b31cd97c7fa1f4481cd68d588419fd45f10ecaee6bc30"}, + {file = "pytest_env-1.1.5.tar.gz", hash = "sha256:91209840aa0e43385073ac464a554ad2947cc2fd663a9debf88d03b01e0cc1cf"}, +] + +[package.dependencies] +pytest = ">=8.3.3" + +[package.extras] +testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "pytest-mock (>=3.14)"] + [[package]] name = "pytest-mock" version = "3.14.0" @@ -380,4 +398,4 @@ files = [ [metadata] lock-version = "2.1" python-versions = ">=3.12, <3.13" -content-hash = "5be5e4e13be93614c6a8f1d722748f3ac25a3c50e59bb8366cdab3312d70e45e" +content-hash = "58fc409de10d9fccc22304b5e3054a1de3c91b70d864121e4abcded535ab0f5b" diff --git a/pyproject.toml b/pyproject.toml index e8d6d60..766c58b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ pylint = "^3.3.6" pytest = "^8.3.5" pytest-cov = "^6.1.1" pytest-mock = "^3.14.0" +pytest-env = "^1.1.5" [build-system] requires = ["poetry-core"] diff --git a/src/data/accel/hbk/aligner.py b/src/data/accel/hbk/aligner.py index ce1b0d8..055a560 100644 --- a/src/data/accel/hbk/aligner.py +++ b/src/data/accel/hbk/aligner.py @@ -4,10 +4,11 @@ import numpy as np # project imports +from data.accel.aligner import IAligner from data.accel.hbk.accelerometer import Accelerometer -class Aligner: +class Aligner(IAligner): def __init__(self, mqtt_client, topics: list, map_size=44840, missing_value=np.nan): """ Initializes the Aligner to receive and align data from multiple MQTT topics. @@ -101,7 +102,7 @@ def _extract_aligned_block(self, group: List[int], batch_size: int, """ aligned_data = [[] for _ in self.channels] samples_collected = 0 - utc_time = datetime.utcnow() + utc_time = datetime.now() for key in group: entries = [ch.get_samples_for_key(key) for ch in self.channels] diff --git a/src/examples/README.md b/src/examples/README.md index 6009825..e272776 100644 --- a/src/examples/README.md +++ b/src/examples/README.md @@ -42,10 +42,16 @@ There are two examples. * **example_2** demonstrates the use of `Aligner` class to collect and align accelerometer measurements from multiple MQTT data streams. -A simple example is provided to run the `main()` function from `experiment_1.py`. +To run these examples, use: -To run this example, use: +```bash +python src/examples/example_1.py +python src/examples/example_2.py +``` + +You can also run these examples in **poetry** environment using ```bash -python examples/example_1.py +poetry run example_1 +poetry run example_2 ``` diff --git a/src/examples/experiment_1.py b/src/examples/experiment_1.py index 2478b0a..4990036 100644 --- a/src/examples/experiment_1.py +++ b/src/examples/experiment_1.py @@ -1,8 +1,9 @@ import time +import sys import numpy as np # pylint: disable=unused-import # Project imports -from data.accel.hbk.accelerometer import Accelerometer # type: ignore +from data.accel.hbk.accelerometer import Accelerometer from data.sources.mqtt import setup_mqtt_client, load_config # type: ignore @@ -31,12 +32,12 @@ def main(): for key, fifo in sorted(accelerometer.data_map.items()): print(f"Key: {key} -> Data: {list(fifo)}\n") _, data = accelerometer.read(requested_samples=256) - print("Data requsted", data) mqtt_client.loop_stop() mqtt_client.disconnect() - time.sleep(1) - print("Exiting cleanly") + + print("Data requsted", data) + sys.stdout.flush() if __name__ == '__main__': main() diff --git a/src/examples/experiment_2.py b/src/examples/experiment_2.py index 73bb233..793c3db 100644 --- a/src/examples/experiment_2.py +++ b/src/examples/experiment_2.py @@ -2,7 +2,7 @@ # Project imports from data.sources.mqtt import setup_mqtt_client, load_config # type: ignore -from data.accel.hbk.aligner import Aligner # type: ignore +from data.accel.hbk.aligner import Aligner def main(): @@ -25,7 +25,7 @@ def main(): aligner = Aligner(mqtt_client, topics=selected_topics, map_size=2560) while True: - time.sleep(1) + time.sleep(1) # Allow time for data collection data, utime = aligner.extract(16) if data.shape[0] == 0: print("Not enough aligned data yet.") diff --git a/tests/integration/data/accel/hbk/test_accelerometer.py b/tests/integration/data/accel/hbk/test_accelerometer.py index 795b3bf..7da78ac 100644 --- a/tests/integration/data/accel/hbk/test_accelerometer.py +++ b/tests/integration/data/accel/hbk/test_accelerometer.py @@ -5,7 +5,7 @@ import os import numpy as np -from data.accel.hbk.accelerometer import Accelerometer # type: ignore +from data.accel.hbk.accelerometer import Accelerometer from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE from data.sources.mqtt import setup_mqtt_client, load_config import uuid diff --git a/tests/integration/data/accel/hbk/test_aligner.py b/tests/integration/data/accel/hbk/test_aligner.py index d446e99..aee1e3d 100644 --- a/tests/integration/data/accel/hbk/test_aligner.py +++ b/tests/integration/data/accel/hbk/test_aligner.py @@ -5,7 +5,7 @@ import struct import numpy as np -from data.accel.hbk.aligner import Aligner # type: ignore +from data.accel.hbk.aligner import Aligner from constants import DESCRIPTOR_LENGTH, METADATA_VERSION, SECONDS, NANOSECONDS, BATCH_SIZE from data.sources.mqtt import setup_mqtt_client, load_config import uuid diff --git a/tests/unit/data/accel/hbk/test_aligner_unit.py b/tests/unit/data/accel/hbk/test_aligner_unit.py index f41f754..77c99fb 100644 --- a/tests/unit/data/accel/hbk/test_aligner_unit.py +++ b/tests/unit/data/accel/hbk/test_aligner_unit.py @@ -1,7 +1,7 @@ import pytest import numpy as np from unittest.mock import MagicMock, patch -from data.accel.hbk.aligner import Aligner # type: ignore +from data.accel.hbk.aligner import Aligner pytestmark = pytest.mark.unit