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How to evaluate a 3D reconstruction and automated measures with a virtual plant as ground truthLink

ObjectiveLink

Quantitative evaluation of a 3D reconstruction and/or automated measure from a phenotyping experiment is critical, from both developer and end-user perspectives. However, obtaining ground truth reference is often tedious (e.g. manual measurements, it must be anticipated (synchronous measures with image acquisition), and some type of data are just inacessible with available technologies (e.g. having a reference point cloud).

Virtual plants makes data acquisition inexpensive and allows to parametrize the type of data. By design, ground truth data can be easily extracted from these virtual datasets. We thus designed the Virtual Plant Imager to take images of any 3D object, as a digital twin of our real plant imager.

After reading this tutorial, you should be able to generate a single virtual plant dataset (including several ground truth reference) in order to evaluate the phenotyping results generated through an analysis pipeline made with our plant-3d-vision tool suite.

PrerequisiteLink

docker_logo We highly recommend the use of docker containers to run ROMI software, if you wish to use the docker images we provide, have a look here.

If it is not already done, you must be able to build and run the docker images of:

  • the (Virtual) Plant Imager by following these instructions. This is required to generate the virtual data (initial plant 3D model, ground truth and RGB images).
  • the plant-3d-vision by following these instructions. This is required to reconstruct a 3D model from the virtual 2D images, as if they were images of real plants. This docker will also allow you to evaluate this reconstruction using the available virtual ground truth data.

Step-by-step tutorialLink

Principle: You want to evaluate the results generated by an analysis pipeline made with our plant-3d-vision tool suite. Let's say that this pipeline is defined by a typical configuration file, test_pipe.toml.

The idea is to generate images of a virtual 3D plant and provide these picture as input to the tested analysis pipeline. Technically, the Virtual Plant Imager relies on Blender v2.81a to generate at set of (2D) RGB images from the plant 3d model, mimicking what a real camera would do on a real plant. Any virtual camera pose can be generated (ie. distance, angle), but virtual poses similar to the real robot (plant imager) are preferred. An HTTP server acts as an interface to drive Blender generation scripts.

The virtual plant 3D model (with some of its ground truth references) can be imported and given as an input. However, we provide an integrated procedure to generate a virtual 3D plant directly "on the fly" with Lpy, using a Lpy model and customizable parameters. Some ground truth references will also be automatically generated.

Once this virtual plant has been virtually imaged, there are all data and metadata required to run an analysis with the tested pipeline. The results of this analysis will be compared to the virtual ground truth. Four type of evaluations are currently implemented :

  • evaluation of a 2D segmentation
  • evaluation of a 3D segmentation of the point cloud
  • comparison of point cloud similarity
  • evaluation of phyllotaxis measures (angles and internodes)

1. Prepare data into a proper databaseLink

First, create a working directory on your host machine, let's say home/host/path/my_virtual_db. You can find an example of such a directory here.

This working directory is a proper "romi" database which contains additional data for the virtual plant generation and/or imaging grouped in a so-called `vscan_data folder:

Legend:

  • (*) the name is fixed and cannot be changed
  • (!) the folder/file must exist (no tag means that the folder is not required for the program to run)
my_virtual_db/
│   romidb (!*) # a (empty) marker file for recognition by the plantdb module
└───vscan_data/ (!*) 
│   └───hdri/ (*)
│       │   hdri_file1.hdr
│       │   hdri_file2.hdr
│       │   etc...
│   └───lpy/ (*)
│       │   my_plant_species_model.lpy
│   └───obj/ (*)
│       │   VirtualPlant.obj
│       │   VirtualPlant_mtl
│   └───metadata/(!*)
│       │   hdri.json
│       │   lpy.json
│       │   obj.json
│       │   palette.json
│       │   scenes.json
│   └───palette/ (*)
│       │   my_plant_species_model.png
│   └───scenes/ (*)
│   files.json

1.1 quick ready-to-use exampleLink

Recommended if you are not familiar with the virtual plant imager. You can directly obtain a functional working directory from the repository of the plant-imager you cloned in your host machine

So if your working directory is named my_virtual_db, execute in a terminal:

cd plant-imager # enter the cloned repository in your host machine
cp -r database_example home/host/path/my_virtual_db
To skip details and directly run the virtual plant imager, go now to section [2.](#2-generate-virtual-images-from-a-lpy-virtual-plant-in-a-virtual-scene)

1.2 Customize data of the virtual plant and/or of the virtual imagesLink

Warning

For advanced users. If you modify data, you most likely need to modify the configuration .toml file downstream.

You can modify and enrich the virtual dataset in several manner (modifying the LPy model and parameters, importing your own model and avoiding Lpy-generation, change background scenes, etc...). For all these options, please refer to the specifications of the virtual plant imager.

2. Generate virtual images from a (Lpy) virtual plant in a virtual sceneLink

Start the docker container of the plant-imager with your database mounted:

cd plant-imager/docker
./run.sh -db /home/host/path/my_virtual_db  # This will map your working databse to the `db` directory located in the docker's user home
Then, in this docker container, generate the virtual dataset by running the following command:

(lpyEnv) user@5c9e389f223d  romi_run_task --config plant-imager/config/vscan_lpy_blender.toml VirtualScan db/my_virtual_plant # Run VirtualScan by specifying the output folder 'my_virtual_plant'

The computation can take a few minutes, depending on your system capacities. if it works, the terminal should display something like that:

===== Luigi Execution Summary =====

Scheduled 4 tasks of which:
* 2 complete ones were encountered:
    - 1 LpyFileset(scan_id=vscan_data)
    - 1 PaletteFileset(scan_id=vscan_data)
* 2 ran successfully:
    - 1 VirtualPlant(...)
    - 1 VirtualScan(...)

This progress looks :) because there were no failed tasks or missing dependencies
Results: in your database, a new folder (here called my_virtual_plant) should have been created, that contain data and metadata related to the virtual image acquisition of this virtual plant !

my_virtual_db
│   romidb
└───vscan_data/
└───my_virtual_plant/
│   ├── images/
│   ├── metadata/
│   │   └── images/
│   │   └── images.json
│   └── files.json
│   └── scan.toml

With the default parameters provided with this example (Lpy model and configuration file), there is only one generated plant, which has the following main characteristics

  • It is a model of an Arabidopsis thaliana plant
  • It has only a main stem and no lateral branches (simplified architecture)
  • It is a mature plant, that has grown an elongated inflorescence stem bearing several mature fruit (called a 'silique', the typical pod of the Brassicaceae family) and still has some flowers at the very tip.

In the next two sections, we point to simple paramaters of the configuration file used for this task to modify either the virtual plant or the virtual imaging.

2.1 (optional) how to modify the virtual plant with LPy parametersLink

Note

Detailed description can be found here

Below are the main lpy parameters that can be customized to change how the virtual plant looks like (age, size, branching, etc...).

[VirtualPlant.lpy_globals]
BRANCHON = false
MEAN_NB_DAYS = 70
STDEV_NB_DAYS = 5
BETA = 51
INTERNODE_LENGTH = 1.3
STEM_DIAMETER = 0.09

2.2 (optional) how to modify the virtual imaging performed by the virtual imagerLink

Note

Detailed description can be found here

Below are the main lpy parameters that can be customized to change how the virtual images are taken (path, background scenes, resolution, etc...)

virtual camera path [ScanPath] class_name = "Circle" [ScanPath.kwargs] center_x = -2 center_y = 3 z = 65 tilt = 8 radius = 75 n_points = 18

3. Running a reconstruction pipeline on the virtual datasetLink

Once you have a virtual dataset of images that all look like a real one, you can analyze it like a real one with romi pipelines from our plant-3d-vision tool suite !

Remember that the pipeline you want to evaluate is defined by the following configuration file: test_pipe.toml.

To adapt to the virtual imaging and focus the evaluation to the downstream image analysis and 3D reconstruction, you can adapt the configuration file to include ground truth from virtual imaging to use ground truth poses. Create a new configuration file for the evaluation and modify it as follows:

cp test_pipe.toml test_pipe_veval.toml #copy and rename the configuration file of the pipeline you want to test 
In the newly created test_pipe_veval.toml, deactivate use of colmap poses for the volume carving algorithm ([Voxel] Task of the pipeline).
[Voxels]
use_colmap_poses = false
[Masks]
upstream_task = Scan

Then the analysis pipeline can be run as usual except that colmap will not be run :

romi_run_task \ #romi pipeline scheduler 
--config path/to/test_pipe_veval.toml \ # configuration of the pipeline to evaluate
AnglesAndInternodes \ #Last task to execute
/path/to/my_virtual_plant #folder inside the database on which the analysis will be run

This run should process all dependencies and generates notably a segmented point cloud and measures of the phyllotaxis (angles and internodes) !

Note

any available romi Tasks for image analysis can be runned here. Please refer to the list of Tasks implemented in our romi software suite.

Note

The command line can be executed in docker container or in a terminal if you have activated the correct virtual environments and proceeded to local installation of the software.

Please refer to this tutorial if you encounter problems to run pipeline from our plant-3d-vision tool suite.

After execution, the terminal should display luigi execution summary, as in this example:

===== Luigi Execution Summary =====

Scheduled 8 tasks of which:
* 2 complete ones were encountered:
    - 1 ImagesFilesetExists(scan_id=, fileset_id=images)
    - 1 ModelFileset(scan_id=models)
* 6 ran successfully:
    - 1 AnglesAndInternodes(...)
    - 1 OrganSegmentation(scan_id=, upstream_task=SegmentedPointCloud, eps=2.0, min_points=5)
    - 1 PointCloud(...)
    - 1 Segmentation2D(...)
    - 1 SegmentedPointCloud(scan_id=, upstream_task=PointCloud, upstream_segmentation=Segmentation2D, use_colmap_poses=False)
    ...

This progress looks :) because there were no failed tasks or missing dependencies

===== Luigi Execution Summary =====
Results: new subfolders and metadata resulting from the analysis should have been created in the folder of the analyzed plant dataset (called my_virtual_plant in this example).

The particular data generated depends on the pipeline you called. We provide an example here with a pipeline involving machine-learning based segmentation of 2D images and proceeding up to phyllotaxis measures (angles & internodes.)

legend: * (.) indicates data that were already present before the run of the pipeline (but the data content may have been modified) * folder names generated by the analysis generally start with the corresponding Task name end with a hashcode to keep track of task execution by the Luigi scheduler (e.g. _1_0_2_0_0_1_5f7aad388e). Such code is replaced by '_hashcode' suffix in the example below

my_virtual_db
│   romidb (.)
└───vscan_data/ (.)
└───my_virtual_plant/ (.)
│   ├── images/ (.)
│   ├── metadata/ (.)
│   ├── AnglesAndInternodes_hashcode/
│   ├── OrganSegmentation_hashcode/
│   ├── PointCloud_hashcode/
│   ├── Segmentation2D_hashcode/
│   ├── PointCloudGroundTruth_100000__VirtualPlantObj_hashcode/
│   ├── SegmentedPointCloud__Segmentation2D_PointCloud_3a1e8e0010/
│   ├── VirtualPlant/
│   ├── VirtualPlant_arabidopsis_note___BRANCHON___fal___angles____inte_hashcode/
│   ├── Voxels_False___background_____False_hashcode/
│   └── files.json (.)
│   └── scan.toml (.)
│   └── pipeline.toml

4. Evaluate the quality of the construction by comparing to the virtual ground truth dataLink

(work in progress)

Once the analysis results are generated, you can now compare this results to the expected ground truth reference of the virtual plant.

Several Evaluation Tasks have been developed by romi: check the list to know which results are evaluating each of them.

In the below example, we would like to evaluate the point-cloud reconstruction, so we run:

romi_run_task \ #romi pipeline scheduler 
--config path/to/test_pipe_veval.toml \ # configuration of the pipeline to evaluate 
PointCloudEvaluation \ #evaluation task of to run
/path/to/my_virtual_plant #analyzed data folder of the database that you want to evaluate

Note

Please refer to this [tutorial] if you encounter problems to run pipeline from our plant-3d-vision tool suite.

5. View and scrutinize in 3D all data generated (images, reconstruction and evaluation)Link

(work in progress) Use of the plant-3d-explorer