initial commit

README.md

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+# flo-data-analysis
+
+Data analysis for [FLO](https://github.com/strawlab/flo).
+
+## Directories
+
+- `load_floz` load data saved by FLO into Python
+- `flo-px4-merge` merge data saved by FLO with data saved by a PX4 flight controller

flo-px4-merge/.gitignore

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+output

flo-px4-merge/Makefile

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+default: output/20240712-134130.gpx
+
+output/20240712-134130.rrd: merge_ulog_floz.py demo-data/20240712-134130.yaml
+	python merge_ulog_floz.py demo-data/20240712-134130.yaml
+
+output/20240712-134130.gpx: output/20240712-134130.rrd smooth_bee_traj.py demo-data/20240712-134130.yaml
+	python smooth_bee_traj.py demo-data/20240712-134130.yaml

flo-px4-merge/README.md

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+# FLO PX4 merge
+
+Merge data from FLO and PX4 flight logs to allow georeferencing of data saved by FLO.
+
+Pan, tilt and distance estimates from FLO are converted from their intrinsic
+quadcopter-centric to georeferenced coordinates first by converting them to the
+local coordinate frame used by the quadcopter’s flight controller. Local
+coordinates are then converted to global coordinates using the PX4 reference
+point (local NED frame origin) in global (GPS / WGS84) frame.
+
+## data acquisition
+
+Ideally, the PX4 flight controller is logging at high rate but the defaults are
+relatively slow.
+
+As a solution, set the PX4 parameter
+[`SDLOG_PROFILE`](https://docs.px4.io/main/en/advanced_config/parameter_reference.html#SDLOG_PROFILE)
+to a value of 4 (high rate).
+
+Alternatively, following [these
+instructions](https://docs.px4.io/main/en/dev_log/logging.html), high data rate
+logs can be enabled by setting `etc/logging/logger_topics.txt` to the following:
+
+```
+vehicle_local_position
+vehicle_gps_position
+vehicle_attitude
+```
+
+However, this disables all other logging, which makes the logs largely useless
+for many other purposes. Thus, we suggest changing the `SDLOG_PROFILE` parameter
+as described above.
+
+## setup
+
+```
+conda create -n px4-log-analysis python=3.11
+pip install pyulog # Used 1.1.0
+pip install matplotlib # Used 3.9.1
+pip install pandas # Used 2.2.2
+pip install PyYAML # Used 6.0.1
+pip install rerun-sdk # Used 0.17.0
+pip install scipy # Used 1.14.0
+pip install adskalman # Used 0.3.11
+pip install imageio # Used 2.34.2
+pip install pyned2lla # Used 0.1.0
+pip install load_floz # Used 0.1.0
+```
+
+## run
+
+```
+conda activate px4-log-analysis
+```

flo-px4-merge/config_loader.py

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+import yaml
+import os
+
+class ConfigLoader:
+    def __init__(self, path: str):
+        self.conf_path, _ = os.path.split(os.path.abspath(path))
+        self.conf = yaml.safe_load(open(path).read())
+        self.conf_filename = path
+        _, filename = os.path.split(path)
+        self.name, _ = os.path.splitext(filename)
+        self.output_dir = self.get_filename('output_dir')
+
+    def _rel_to_abs(self, path: str) -> str:
+        """convert relative paths to absolute paths"""
+        if not os.path.isabs(path):
+            path = os.path.join(self.conf_path, path)
+        return path
+    def get_filename(self, key: str) -> str | None:
+        """get a key as a filename
+
+        return None if the key is not set
+        """
+        path = self.conf.get(key)
+        if path is not None:
+            path = self._rel_to_abs(path)
+        return path
+    def __getitem__(self, key):
+        return self.conf.__getitem__(key)
+    def get(self, *args, **kwargs):
+        return self.conf.get(*args, **kwargs)
+    def out_filename(self, ext: str) -> str:
+        return os.path.join(self.output_dir, self.name+ext)

flo-px4-merge/demo-data/20240712-134130-mask.csv

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+mask_start,mask_end
+2024-07-12 11:41:30.692388352Z,2024-07-12 11:42:00.209415Z
+2024-07-12 11:41:59.425Z,2024-07-12 11:42:00.123Z
+2024-07-12 11:42:19.313686Z,2024-07-12 11:42:20.176216Z
+2024-07-12 11:42:27.438Z,2024-07-12 11:42:31.251Z
+2024-07-12 11:42:37.754Z,2024-07-12 11:42:39.404Z
+2024-07-12 11:43:28.034705Z,2024-07-12 11:43:29.029286Z
+2024-07-12 11:43:34.050221Z,2024-07-12 11:43:34.537991Z
+2024-07-12 11:43:40.773324Z,2024-07-12 11:43:41.193492Z
+2024-07-12 11:43:42.473247Z,2024-07-12 11:43:43.260954Z
+2024-07-12 11:43:53.005133Z,2024-07-12 11:43:53.612814Z
+2024-07-12 11:43:53.736896Z,2024-07-12 11:43:54.163695Z
+2024-07-12 11:43:55.315518Z,2024-07-12 11:43:55.766920Z
+2024-07-12 11:43:56.415569Z,2024-07-12 11:43:57.939959Z
+2024-07-12 11:43:58.996902Z,2024-07-12 11:43:59.548532Z
+2024-07-12 11:44:04.808324Z,2024-07-12 11:44:05.106669Z
+2024-07-12 11:44:05.233765Z,2024-07-12 11:44:05.538626Z
+2024-07-12 11:44:05.927869Z,2024-07-12 11:44:06.272200Z
+2024-07-12 11:44:06.187658Z,2024-07-12 11:44:09.689940Z
+2024-07-12 11:44:11.689740Z,2024-07-12 11:44:13.456619Z
+2024-07-12 11:44:23.721634Z,2024-07-12 11:44:24.222459Z

flo-px4-merge/demo-data/20240712-134130.yaml

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+# data from FLO methods paper
+ulog_file: log_34_2024-7-12-13-45-18.ulg
+floz_file: flo20240712_134130.684896145.floz
+mask_file: 20240712-134130-mask.csv
+output_dir: ../output
+
+recording_id: b7ba4662-2fd5-49c6-8fb9-f961a8f596b4 # autogenerated if not set
+flo_resample_rate: 10.0 # 10 Hz
+timestamp_tolerance_dt: 0.1 # 100 msec
+kalman_smoothing_dt: 0.1 # 100 msec