h5-info-pkg-inra-phenome 1.1.9

Utility package for extracting, reading and saving metadata from HDF5 Phenomobile V2 acquisition file

H5Info Package

This Python package contains the necessary tools to extract data and metadata from HDF5 files generated by Phenomobile acquisition in the context of the Phenome project by INRA, France.

The API of the H5Info package exposes 3 methods:

• load_data(): to extract data from a HDF5 file and store it into a H5Info structure
• save_metadata(): to save a H5Info metadata structure into a JSON file
• load_metadata(): to load a H5Info metadata structure from a JSON file

If an error occurs because of invalid data, a DataError exception is raised. A good practice consists in catching this error in a separate except block than the other exceptions.

Please refer to the main.py script for an example about how to use these three methods.

Install H5Info module

The H5Info module is deployed on PyPi (Python Package Index) under the name h5-info-pkg-inra-phenome.

To install the H5Info module on your local environment, just run the following command:

pip install h5-info-pkg-inra-phenome

H5Info Structure Example

h5_info = H5Info()

Session

• h5_info.session.date = 2020-02-03_09:45:23
• h5_info.session.experiment_id = "2019_SunRise"
• h5_info.session.experiment_uri = "http://www.phenome-fppn.fr/diaphen/2019/v1901"
• h5_info.session.local_infra = "Diaphen"
• h5_info.session.national_infra = "PHENOME"

Plot

• h5_info.plot.id = "20LP4_129_8_1039"
• h5_info.plot.uri = "http://www.phenome-fppn.fr/diaphen/2018/v1801"
• h5_info.plot.coordinates = [[1.5015271931087, 43.532682695713], [1.5015062032854, 43.532676540606], [1.5014877113578, 43.532709920144], [1.5015087011914, 43.532716075254]]
• h5_info.plot.orientation = 158.04785481961858

Vector

• h5_info.vector.id = "Phenomobile V2"
• h5_info.vector.uri = "http://www.phenome-fppn.fr/diaphen/2018/v1801"
• h5_info.vector.serial_nb = "PHENOMOBILE_V2_01"

Sensors

for sensor in h5_info.sensors:

• sensor.id = "4"
• sensor.type = "camera"
• sensor.description = "camera_1"
• sensor.manufacturer = "Baumer"
• sensor.model = "VLG 40C"
• sensor.serial_nb = "00_06_be_01_62_f0"
• sensor.uri = "http://www.phenome-fppn.fr/agrophen/2019/s19003"

Image

for image in sensor:

• image.name = "camera_1_1"
• image.date = 2019-06-04_12:11:52.316072

Camera, Multispectral and Lidar images have also their own specific attributes.

Others fields

The H5Info structure contains other fields not detailed here, such as the vector position, each sensor positions and static transforms factors. In addition, a geolocalisation file containing positions of the head is saved in a separate file named geo.csv