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6cc1f1d
init metadata ros to omh converter
Alizzie b2b12f2
generalize raw biosignal body msg
Alizzie 26c818f
simple main script converting omh biosignals body to ros
Alizzie 014da96
draft main script converting biosignals (body + meta) to ros
Alizzie 0ed3239
draft main script converting biosignals (body + meta) to ros
Alizzie d81510e
create new folder with json to ros msg generator
Alizzie 145be33
fix module and add noteboook example
Alizzie 1db31c7
fix module and add noteboook example
Alizzie 4a1b436
change folder structure, and adapt omh to ros message generator
Alizzie 9c5d63e
revert submodule usage
Alizzie d03045c
install directly ord schema package
Alizzie 9c6cd3a
show all functions how to use ord_schema package
Alizzie 9566833
update omh_schema_to_ros_message notebook
Alizzie 3eb30a1
Moved streamer to root dir
moperezs 610a774
delete test schema and test generated messages from omh_ros_converter…
Alizzie da1fb27
add ending new line at generated ros messages
Alizzie e5a7684
Update offline_converter/omh_to_ros_schema/converters/__init__.py
Alizzie b2b70c5
rename bcg example file
Alizzie 95c720d
rename eog example filename
Alizzie 3efe209
remove wildcards
Alizzie 6c85025
Update offline_converter/omh_to_ros_schema/utils/__init__.py
Alizzie 56c623c
add ending new line in files
Alizzie c9deca2
use linter and formatter
Alizzie 9ade150
Merge branch 'origin/feature/omhToRosDev' of https://github.com/SCAI-…
Alizzie 687e956
fix input/output types in offline converters
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| # Python packaging | ||
| *.egg-info/ | ||
| dist/ | ||
| build/ | ||
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| # Virtual environments | ||
| .venv/ | ||
| venv/ | ||
| env/ | ||
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| # Bytecode cache | ||
| __pycache__/ | ||
| *.py[cod] | ||
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| # Editor/IDE junk | ||
| .vscode/ | ||
| .idea/ | ||
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| # OS files | ||
| .DS_Store | ||
| Thumbs.db |
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| # healthcare_common | ||
| # healthcare_common | ||
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| ## Installation | ||
| pip install -e . | ||
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| std_msgs/Header header | ||
| string session_id # match BCGInfo's session_id (if used) | ||
| int32 sample_size | ||
| float32[] bcg # Raw or filtered BCG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| # Sensor_placement Enum | ||
| uint8 SENSOR_PLACEMENT_UNKNOWN = 0 | ||
| uint8 SENSOR_PLACEMENT_CHEST = 2 | ||
| uint8 SENSOR_PLACEMENT_BACK = 3 | ||
| uint8 SENSOR_PLACEMENT_MATTRESS = 4 | ||
| uint8 SENSOR_PLACEMENT_CHAIR = 5 | ||
| uint8 SENSOR_PLACEMENT_FEET = 6 | ||
| uint8 SENSOR_PLACEMENT_WRIST = 7 | ||
| uint8 SENSOR_PLACEMENT_ARM = 8 | ||
| uint8 SENSOR_PLACEMENT_DESK = 9 | ||
| uint8 SENSOR_PLACEMENT_CLOTHING = 10 | ||
| uint8 SENSOR_PLACEMENT_CUSTOM = 255 | ||
| uint8 sensor_placement # Sensor Placements | ||
| # Sensing_direction Enum | ||
| uint8 SENSING_DIRECTION_DORSO_VENTRAL = 1 | ||
| uint8 SENSING_DIRECTION_LONGITUDINAL = 2 | ||
| uint8 SENSING_DIRECTION_MEDIO_LATERAL = 3 | ||
| uint8 SENSING_DIRECTION_UNKNOWN = 0 | ||
| uint8 sensing_direction # Axis along which BCG is measured | ||
| # Sensing_modality Enum | ||
| uint8 SENSING_MODALITY_PIEZOELECTRIC_FILM = 1 | ||
| uint8 SENSING_MODALITY_FORCEPLATE = 2 | ||
| uint8 SENSING_MODALITY_ACCELEROMETER = 3 | ||
| uint8 SENSING_MODALITY_PIEZOELECTRIC_CRYSTAL = 4 | ||
| uint8 SENSING_MODALITY_UNKNOWN = 0 | ||
| uint8 sensing_modality # Type of Sensor used | ||
| # Measurement_system Enum | ||
| uint8 MEASUREMENT_SYSTEM_STARR = 1 | ||
| uint8 MEASUREMENT_SYSTEM_NICKERSON = 2 | ||
| uint8 MEASUREMENT_SYSTEM_DOCK = 3 | ||
| uint8 MEASUREMENT_SYSTEM_OTHER = 4 | ||
| uint8 MEASUREMENT_SYSTEM_UNKNOWN = 0 | ||
| uint8 measurement_system # System Type |
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| std_msgs/Header header | ||
| string device_manufacturer | ||
| string device_name | ||
| string device_type | ||
| string device_serial_number |
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| std_msgs/Header header | ||
| string session_id # match ECGInfo's session_id (if used) | ||
| int32 channel_size | ||
| int32 sample_size | ||
| float32[] ecg # Raw or filtered ECG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Lead_type Enum | ||
| uint8 LEAD_TYPE_I = 1 | ||
| uint8 LEAD_TYPE_II = 2 | ||
| uint8 LEAD_TYPE_III = 3 | ||
| uint8 LEAD_TYPE_AVR = 4 | ||
| uint8 LEAD_TYPE_AVL = 5 | ||
| uint8 LEAD_TYPE_AVF = 6 | ||
| uint8 LEAD_TYPE_V1 = 7 | ||
| uint8 LEAD_TYPE_V2 = 8 | ||
| uint8 LEAD_TYPE_V3 = 9 | ||
| uint8 LEAD_TYPE_V4 = 10 | ||
| uint8 LEAD_TYPE_V5 = 11 | ||
| uint8 LEAD_TYPE_V6 = 12 | ||
| uint8 LEAD_TYPE_UNKNOWN = 0 | ||
| uint8 LEAD_TYPE_CUSTOM = 255 | ||
| uint8 lead_type # Standard ECG lead names according to clinical conventions (12-lead and extended leads). |
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| std_msgs/Header header | ||
| string session_id # match EdaInfo's session_id (if used) | ||
| int32 sample_size | ||
| float32[] scl # Skin Conductance Level (tonic) | ||
| float32[] scr # Skin Conductance Response (phasic) | ||
| float32[] eda # Sum of signals (scl + scr) | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Electrode_type Enum | ||
| uint8 ELECTRODE_TYPE_UNKNOWN = 0 | ||
| uint8 ELECTRODE_TYPE_SURFACE = 2 | ||
| uint8 ELECTRODE_TYPE_INTRACUTANEOUS = 3 | ||
| uint8 ELECTRODE_TYPE_CUSTOM = 255 | ||
| uint8 electrode_type | ||
| # Measuring_technique Enum | ||
| uint8 MEASURING_TECHNIQUE_UNKNOWN = 0 | ||
| uint8 MEASURING_TECHNIQUE_ENDOSOMATIC = 2 | ||
| uint8 MEASURING_TECHNIQUE_EXOSOMATIC = 3 | ||
| uint8 MEASURING_TECHNIQUE_CUSTOM = 255 | ||
| uint8 measuring_technique | ||
| # Current_form Enum | ||
| uint8 CURRENT_FORM_UNKNOWN = 0 | ||
| uint8 CURRENT_FORM_DC = 2 | ||
| uint8 CURRENT_FORM_AC = 3 | ||
| uint8 current_form |
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| std_msgs/Header header | ||
| string session_id # match EEGInfo's session_id (if used) | ||
| int32 channel_size | ||
| int32 sample_size | ||
| float32[] eeg # Raw or filtered EEG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Electrode_site Enum | ||
| uint8 ELECTRODE_SITE_UNKNOWN = 0 | ||
| uint8 ELECTRODE_SITE_FP1 = 2 | ||
| uint8 ELECTRODE_SITE_FP2 = 3 | ||
| uint8 ELECTRODE_SITE_F3 = 4 | ||
| uint8 ELECTRODE_SITE_F4 = 5 | ||
| uint8 ELECTRODE_SITE_C3 = 6 | ||
| uint8 ELECTRODE_SITE_C4 = 7 | ||
| uint8 ELECTRODE_SITE_P3 = 8 | ||
| uint8 ELECTRODE_SITE_P4 = 9 | ||
| uint8 ELECTRODE_SITE_O1 = 10 | ||
| uint8 ELECTRODE_SITE_O2 = 11 | ||
| uint8 ELECTRODE_SITE_F7 = 12 | ||
| uint8 ELECTRODE_SITE_F8 = 13 | ||
| uint8 ELECTRODE_SITE_T3 = 14 | ||
| uint8 ELECTRODE_SITE_T4 = 15 | ||
| uint8 ELECTRODE_SITE_T5 = 16 | ||
| uint8 ELECTRODE_SITE_T6 = 17 | ||
| uint8 ELECTRODE_SITE_FZ = 18 | ||
| uint8 ELECTRODE_SITE_CZ = 19 | ||
| uint8 ELECTRODE_SITE_PZ = 20 | ||
| uint8 ELECTRODE_SITE_OZ = 21 | ||
| uint8 ELECTRODE_SITE_CUSTOM = 255 | ||
| uint8 electrode_site | ||
| # Electrode_physical_type Enum | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_UNKNOWN = 0 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_AGCL = 2 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_GOLD_CUP = 3 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_DRY = 4 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_WET = 5 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_HYDROGEL = 6 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_MICRONEEDLE = 7 | ||
| uint8 ELECTRODE_PHYSICAL_TYPE_CUSTOM = 255 | ||
| uint8 electrode_physical_type | ||
| # Signal_mode Enum | ||
| uint8 SIGNAL_MODE_UNKNOWN = 0 | ||
| uint8 SIGNAL_MODE_SURFACE = 2 | ||
| uint8 SIGNAL_MODE_INTRACRANIAL = 3 | ||
| uint8 SIGNAL_MODE_CUSTOM = 255 | ||
| uint8 signal_mode |
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| std_msgs/Header header | ||
| string session_id # match EMGInfo's session_id (if used) | ||
| int32 channel_size | ||
| int32 sample_size | ||
| float32[] emg # Raw or filtered EMG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Electrode_type Enum | ||
| uint8 ELECTRODE_TYPE_UNKNOWN = 0 | ||
| uint8 ELECTRODE_TYPE_SURFACE = 2 | ||
| uint8 ELECTRODE_TYPE_NEEDLE = 3 | ||
| uint8 ELECTRODE_TYPE_WIRE = 4 | ||
| uint8 ELECTRODE_TYPE_INTERFERENTIAL = 5 | ||
| uint8 ELECTRODE_TYPE_CUSTOM = 255 | ||
| uint8 electrode_type | ||
| # External_device Enum | ||
| uint8 EXTERNAL_DEVICE_UNKNOWN = 0 | ||
| uint8 EXTERNAL_DEVICE_TENS = 2 | ||
| uint8 EXTERNAL_DEVICE_FES = 3 | ||
| uint8 EXTERNAL_DEVICE_EMG_TRIGGER = 4 | ||
| uint8 EXTERNAL_DEVICE_CUSTOM = 255 | ||
| uint8 external_device | ||
| # Signal_mode Enum | ||
| uint8 SIGNAL_MODE_UNKNOWN = 0 | ||
| uint8 SIGNAL_MODE_SURFACE = 2 | ||
| uint8 SIGNAL_MODE_INTRAMUSCULAR = 3 | ||
| uint8 SIGNAL_MODE_CUSTOM = 255 | ||
| uint8 signal_mode |
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| std_msgs/Header header | ||
| string session_id # match EOGInfo's session_id (if used) | ||
| int32 channel_size | ||
| int32 sample_size | ||
| float32[] eog # Raw or filtered EOG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Lead_type Enum | ||
| uint8 LEAD_TYPE_UNKNOWN = 0 | ||
| uint8 LEAD_TYPE_BIPOLAR_HORIZONTAL = 2 | ||
| uint8 LEAD_TYPE_BIPOLAR_VERTICAL = 3 | ||
| uint8 LEAD_TYPE_UNIPOLAR = 4 | ||
| uint8 LEAD_TYPE_CORNEAL_RETINAL = 5 | ||
| uint8 LEAD_TYPE_CUSTOM = 255 | ||
| uint8 lead_type | ||
| # Signal_mode Enum | ||
| uint8 SIGNAL_MODE_UNKNOWN = 0 | ||
| uint8 SIGNAL_MODE_SURFACE = 2 | ||
| uint8 SIGNAL_MODE_BIPOLAR = 3 | ||
| uint8 SIGNAL_MODE_UNIPOLAR = 4 | ||
| uint8 SIGNAL_MODE_CORNEAL_RETINAL = 5 | ||
| uint8 SIGNAL_MODE_INTRACULAR = 6 | ||
| uint8 SIGNAL_MODE_DERIVED = 7 | ||
| uint8 SIGNAL_MODE_CUSTOM = 255 | ||
| uint8 signal_mode | ||
| # Lightsource Enum | ||
| uint8 LIGHTSOURCE_UNKNOWN = 0 | ||
| uint8 LIGHTSOURCE_TUNGSTEN = 2 | ||
| uint8 LIGHTSOURCE_HALOGEN = 3 | ||
| uint8 LIGHTSOURCE_LED = 4 | ||
| uint8 LIGHTSOURCE_FLUORESCENT = 5 | ||
| uint8 LIGHTSOURCE_SUNLIGHT = 6 | ||
| uint8 LIGHTSOURCE_CUSTOM = 255 | ||
| uint8 lightsource | ||
| float32 gazefield # gazefield (unit: cd/m^2) | ||
| float32[] light_dark_phase |
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| std_msgs/Header header | ||
| string session_id # match ICGInfo's session_id (if used) | ||
| int32 sample_size | ||
| float32[] icg # Raw or filtered ICG values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| string[] electrode_placement # Support multiple electrode placements | ||
| # Lead_type Enum | ||
| uint8 LEAD_TYPE_UNKNOWN = 0 | ||
| uint8 LEAD_TYPE_TRANSTHORACIC = 2 | ||
| uint8 LEAD_TYPE_FOUR_ELECTRODE = 3 | ||
| uint8 LEAD_TYPE_SIX_ELECTRODE = 4 | ||
| uint8 LEAD_TYPE_SPOT = 5 | ||
| uint8 LEAD_TYPE_CUSTOM = 255 | ||
| uint8 lead_type | ||
| # Technique Enum | ||
| uint8 TECHNIQUE_UNKNOWN = 0 | ||
| uint8 TECHNIQUE_TETRAPOLAR = 2 | ||
| uint8 TECHNIQUE_OCTAPOLAR = 3 | ||
| uint8 TECHNIQUE_CUSTOM = 255 | ||
| uint8 technique |
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7
examples/notebooks/generated_ros_msgs/MeasurementSpecification.msg
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| std_msgs/Header header | ||
| float32 accuracy | ||
| float32 min_measuring_value_range # Minimal measuring value range | ||
| float32 max_measuring_value_range # Maximal measuring value range | ||
| float32 gain | ||
| int32 adc_resolution | ||
| float32 resolution |
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| std_msgs/Header header | ||
| float32 min_value # The minimum value. | ||
| float32 max_value # The maximum value. | ||
| string unit # The unit of measure of the element. Allowed values are drawn from the Common synonyms (non-UCUM) column of [subset of] UCUM, SI and English units. |
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7
examples/notebooks/generated_ros_msgs/OperatingEnvironment.msg
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| std_msgs/Header header | ||
| float32 battery_level # battery level (unit: %) | ||
| float32 min_operation_temperature # Minimal operation temperature | ||
| float32 max_operation_temperature # Maximal operation temperature | ||
| float32 maximal_relative_humidity # maximal relative humidity (unit: %) | ||
| float32 min_atmospheric_pressure # Minimal atmospheric pressure (unit: atm) | ||
| float32 max_atmospheric_pressure # Maximal atmospheric pressure (unit: atm) |
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13
examples/notebooks/generated_ros_msgs/OrdDefaultHeader.msg
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| std_msgs/Header header | ||
| string uuid # The identifier of this data point: a globally unique value, generated using RFC 4122 approach. | ||
| string namespace # The namespace of the schema. A namespace serves to disambiguate schemas with conflicting names. | ||
| string name # The name of the schema. | ||
| string version # The version of the schema, e.g. 1.0. | ||
| string source_creation_date_time # This schema represents a point in time (ISO8601). If a timezone is not included, the timezone is assumed to be UTC. | ||
| # Modality Enum | ||
| uint8 MODALITY_SENSED = 1 | ||
| uint8 MODALITY_SELF-REPORTED = 2 | ||
| uint8 modality # The modality whereby the measure is obtained, e.g., sensed or self-reported | ||
| float32 number_of_times | ||
| string time_window | ||
| string[] external_datasheets # Reference(s) to external documentation regarding the component(s) relevant to describe the collection, computation, use, etc. of this datapoint or data series, e.g., software, algorithm, study protocol, etc. |
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| std_msgs/Header header | ||
| string session_id # match PPGInfo's session_id (if used) | ||
| int32 sample_size | ||
| int32 wavelength_size | ||
| float32 ac_component # # [samples]×[wavelengths] | ||
| float32 dc_component # # [samples]×[wavelengths] | ||
| float32[] ppg # Raw or filtered PPF values | ||
| float32[] signal_quality # From 0 (poor) to 1 [%] |
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| SensorDeviceMetadata sensor_Device_Metadata | ||
| # Sensor_placement Enum | ||
| uint8 SENSOR_PLACEMENT_UNKNOWN = 0 | ||
| uint8 SENSOR_PLACEMENT_FINGER = 2 | ||
| uint8 SENSOR_PLACEMENT_WRIST = 3 | ||
| uint8 SENSOR_PLACEMENT_EARLOBE = 4 | ||
| uint8 SENSOR_PLACEMENT_FOREHEAD = 5 | ||
| uint8 SENSOR_PLACEMENT_TOE = 6 | ||
| uint8 SENSOR_PLACEMENT_ARM = 7 | ||
| uint8 SENSOR_PLACEMENT_CHEST = 8 | ||
| uint8 SENSOR_PLACEMENT_ANKLE = 9 | ||
| uint8 SENSOR_PLACEMENT_NOSE = 10 | ||
| uint8 SENSOR_PLACEMENT_PALM = 11 | ||
| uint8 SENSOR_PLACEMENT_SOLE = 12 | ||
| uint8 SENSOR_PLACEMENT_CUSTOM = 255 | ||
| uint8 sensor_placement | ||
| # Measuring_mode Enum | ||
| uint8 MEASURING_MODE_UNKNOWN = 0 | ||
| uint8 MEASURING_MODE_TRANSMISSIVE_ABSORPTION = 2 | ||
| uint8 MEASURING_MODE_REFLECTIVE = 3 | ||
| uint8 MEASURING_MODE_CUSTOM = 255 | ||
| uint8 measuring_mode | ||
| int32[] wavelengths_mm # Nanometer value for each channel, may be [660, 880, 940] | ||
| # Wavelengths_labels Enum | ||
| uint8 WAVELENGTHS_LABELS_UNKNOWN = 0 | ||
| uint8 WAVELENGTHS_LABELS_GREEN = 2 | ||
| uint8 WAVELENGTHS_LABELS_RED = 3 | ||
| uint8 WAVELENGTHS_LABELS_IR = 4 | ||
| uint8 WAVELENGTHS_LABELS_BLUE = 5 | ||
| uint8 WAVELENGTHS_LABELS_YELLOW = 6 | ||
| uint8 WAVELENGTHS_LABELS_CUSTOM = 255 | ||
| uint8 wavelengths_labels # Wavelength Label for each channel (optional) |
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20
examples/notebooks/generated_ros_msgs/SensorDeviceHeader.msg
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| std_msgs/Header header | ||
| string device_manufacturer | ||
| string device_name | ||
| string device_type | ||
| string device_serial_number | ||
| float32 battery_level # battery level (unit: %) | ||
| float32 min_operation_temperature # Minimal operation temperature | ||
| float32 max_operation_temperature # Maximal operation temperature | ||
| float32 maximal_relative_humidity # maximal relative humidity (unit: %) | ||
| float32 min_atmospheric_pressure # Minimal atmospheric pressure (unit: atm) | ||
| float32 max_atmospheric_pressure # Maximal atmospheric pressure (unit: atm) | ||
| float32 accuracy | ||
| float32 min_measuring_value_range # Minimal measuring value range | ||
| float32 max_measuring_value_range # Maximal measuring value range | ||
| float32 gain | ||
| int32 adc_resolution | ||
| float32 resolution | ||
| string session_id | ||
| float32 window_size_samples | ||
| float32 quality_window_size_samples |
20 changes: 20 additions & 0 deletions
20
examples/notebooks/generated_ros_msgs/SensorDeviceMetadata.msg
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| std_msgs/Header header | ||
| string device_manufacturer | ||
| string device_name | ||
| string device_type | ||
| string device_serial_number | ||
| float32 battery_level # battery level (unit: %) | ||
| float32 min_operation_temperature # Minimal operation temperature | ||
| float32 max_operation_temperature # Maximal operation temperature | ||
| float32 maximal_relative_humidity # maximal relative humidity (unit: %) | ||
| float32 min_atmospheric_pressure # Minimal atmospheric pressure (unit: atm) | ||
| float32 max_atmospheric_pressure # Maximal atmospheric pressure (unit: atm) | ||
| float32 accuracy | ||
| float32 min_measuring_value_range # Minimal measuring value range | ||
| float32 max_measuring_value_range # Maximal measuring value range | ||
| float32 gain | ||
| int32 adc_resolution | ||
| float32 resolution | ||
| string session_id | ||
| float32 window_size_samples | ||
| float32 quality_window_size_samples |
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I would remove this .gitignore from the repo and let everyone have their custom configs if needed.