How-to import files in ROMI database

Importing external images as a dataset

In order to be able to use external images, i.e. images that were not acquired with the software & hardware developed by ROMI, we provide tools to import them as a scan dataset in the ROMI database.

One example could be a set of pictures (of a plant) acquired with your phone that you would like to reconstruct and maybe analyse with our software.

To do so, you may use the romi_import_folder or romi_import_file executables from plantdb.

For example, you have a set of 10 RGB pictures named img_00*.jpg in a folder my_plant/ that you would like to import as outdoor_plant_1 in a romi database located under /data/romi/db.

First you have to move the pictures to an ìmages sub-directory & create a metadata.json describing the object under study:

cd my_plant
mkdir images
mv *.jpg images/.
touch metadata.json

An example of a metadata.json:

{
    "object": {
        "age": "N/A",
        "culture": "N/A",
        "environment": "outdoor",
        "experiment_id": "romi demo outdoor plant",
        "object": "plant",
        "plant_id": "Chirsuta_1",
        "sample": "whole plant",
        "species": "Cardamine hirsuta",
        "stock": "WT",
        "treatment": "none"
    }
}

To summarize you now should have the following folder structure:

my_plant/
├── images/
│   ├── img_001.jpg
│   ├── [...]
│   └── img_010.jpg
└── metadata.json

Then you can perform the 'import to the database' operation with romi_import_folder:

romi_import_folder my_plant/ìmages/ /data/romi/db/outdoor_plant_1 --metadata my_plant/metadata.json

That's it! Your manual acquisition is ready to be used by the romi_run_task tool for reconstruction.