How to use the `romi_run_task` generic command ?Link

We here assume you followed the "installation instructions" available here.

Getting startedLink

There are some requirements to use the different algorithms in the pipeline. Most of them are installed automatically from the requirements file when using pip. The most important part is Colmap (v3.6).

The two requirements that are not shipped with pip are:

Colmap (v3.6 or v3.7) for the structure from motion algorithms
Blender (>= 2.93) to be able to use the virtual plant imager

Preferably, create a virtual environment for python 3.7 or python 3.8 using virtualenv or a conda environment specific to the 3D Scanner.

Warning

If using python 3.8, Open3D binaries are not yet available on pip, therefore you have to build Open3D from sources!

Basic usageLink

Every task is launched through the romi_run_task command provided in the romitask library. It is a wrapper for luigi, with preloaded tasks from the romitask, plantimager & plant3dvision modules.

The general usage is as follows:

romi_run_task [-h]
              [--config CONFIG]
              [--luigicmd LUIGICMD]
              [--module MODULE]
              [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
              [local-scheduler]
              task
              [dataset_path]

CONFIG is either a file or a folder. If a file, it must be JSON or TOML and contains the configuration of the task to run. If a folder, it will read all configuration files in JSON or TOML format from the folder.
LUIGICMD is an optional parameter specifying an alternative command for luigi.
MODULE is an optional parameter for running task from external modules (see TODO).
LOG_LEVEL is the level of logging. Defaults to INFO, but can be set to DEBUG to increase verbosity.
task is the name of the class to run, see here for a list of task or have a look at the output of romi_run_task -h for a more up-to-date list
dataset_path is the location of the target Scan on which to process the task. It is of the form $ROMI_DB/SCAN_ID, where $ROMI_DB is a path containing the plantdb marker.

Defining the dataset pathLink

To defines the dataset_path you can specify a dataset name like my_scan_007.

You may also use Unix pattern matching with "*" and "?" to select a list of scan dataset. For example, in a DB with the following scan dataset: test_1 my_scan_test, my_scan_002, my_scan_007, my_scan_011

$ROMI_DB/* will match ALL scan dataset
$ROMI_DB/my_scan_* will match my_scan_test, my_scan_002, my_scan_007 & my_scan_011
$ROMI_DB/my_scan_??? will match my_scan_002, my_scan_007 & my_scan_011
$ROMI_DB/my_scan_00? will match my_scan_002 & my_scan_007
$ROMI_DB/my_scan_00* will match my_scan_002 & my_scan_007

Configuration filesLink

The configuration is in the form of a dictionary, in which each key is the ID of a given task.

In TOML format, it reads as follows:

[FirstTask]
parameter1 = value1
parameter2 = value2

[SecondTask]
parameter1 = value1
parameter2 = value2

An example TOML configuration file for the geometric reconstruction pipeline of a point-cloud is:

[Colmap]
upstream_task = "ImagesFilesetExists"
matcher = "exhaustive"
compute_dense = false
align_pcd = true
use_gpu = true
single_camera = true
robust_alignment_max_error = 10

[Undistorted]
upstream_task = "ImagesFilesetExists"

[Masks]
upstream_task = "Undistorted"
query = "{\"channel\":\"rgb\"}"
type = "linear"
parameters = "[0, 1, 0]"
dilation = 3
binarize = true
threshold = 0.2

[Voxels]
upstream_mask = "Masks"
upstream_colmap = "Colmap"
voxel_size = 0.5
type = "carving"

[PointCloud]
upstream_task = "Voxels"
level_set_value = 0.0

To run the full reconstruction pipeline use this configuration file with romi_run_task:

romi_run_task --config scanner.json AnglesAndInternodes /path/to/db/scan_id/ --local-scheduler

This will process all tasks up to the AnglesAndInternodes task. Every task produces a Fileset, a subdirectory in the scan directory whose name starts the same as the task name. The characters following are a hash of the configuration of the task, so that the outputs of the same task with different parameters can coexist in the same scan. Any change in the parameters will make the needed task to be recomputed with subsequent calls of romi_run_task. Already computed tasks will be left untouched.

To recompute a task, just delete the corresponding folder in the scan directory and rerun romi_run_task.

Default task referenceLink

MODULES = {
    # Scanning module:
    "Scan": "plantimager.tasks.scan",
    "ScannerToCenter": "plantimager.tasks.scan",
    "VirtualPlant": "plantimager.tasks.lpy",
    "VirtualScan": "plantimager.tasks.scan",
    "CalibrationScan": "plantimager.tasks.scan",
    "IntrinsicCalibrationScan": "plantimager.tasks.scan",
    # Calibration module:
    "CreateCharucoBoard" : "plant3dvision.tasks.calibration",
    "DetectCharuco" : "plant3dvision.tasks.calibration",
    "ExtrinsicCalibration" : "plant3dvision.tasks.calibration",
    "IntrinsicCalibration" : "plant3dvision.tasks.calibration",
    # Geometric reconstruction module:
    "Colmap": "plant3dvision.tasks.colmap",
    "Undistorted": "plant3dvision.tasks.proc2d",
    "Masks": "plant3dvision.tasks.proc2d",
    "Voxels": "plant3dvision.tasks.cl",
    "PointCloud": "plant3dvision.tasks.proc3d",
    "TriangleMesh": "plant3dvision.tasks.proc3d",
    "CurveSkeleton": "plant3dvision.tasks.proc3d",
    # Machine learning reconstruction module:
    "Segmentation2D": "plant3dvision.tasks.proc2d",
    "SegmentedPointCloud": "plant3dvision.tasks.proc3d",
    "ClusteredMesh": "plant3dvision.tasks.proc3d",
    "OrganSegmentation": "plant3dvision.tasks.proc3d",
    # Quantification module:
    "TreeGraph": "plant3dvision.tasks.arabidopsis",
    "AnglesAndInternodes": "plant3dvision.tasks.arabidopsis",
    # Evaluation module:
    "VoxelsGroundTruth": "plant3dvision.tasks.evaluation",
    "VoxelsEvaluation": "plant3dvision.tasks.evaluation",
    "PointCloudGroundTruth": "plant3dvision.tasks.evaluation",
    "PointCloudEvaluation": "plant3dvision.tasks.evaluation",
    "ClusteredMeshGroundTruth": "plant3dvision.tasks.evaluation",
    "SegmentedPointCloudEvaluation": "plant3dvision.tasks.evaluation",
    "Segmentation2DEvaluation": "plant3dvision.tasks.evaluation",
    "AnglesAndInternodesEvaluation": "plant3dvision.tasks.evaluation",
    "CylinderRadiusGroundTruth": "plant3dvision.tasks.evaluation",
    "CylinderRadiusEstimation": "plant3dvision.tasks.evaluation",
    # Visualization module:
    "Visualization": "plant3dvision.tasks.visualization",
    # Database module:
    "Clean": "romitask.task"
}

Warning

This is for reference only, please update the changes in the code. This will be later replaced by a reference doc generated from the code!

How to use the romi_run_task generic command ?Link