6_Installing_software.rst

Obtaining Pipeline Related Containers

All the code used throughout the pipeline is containerized through Docker and hosted on DockerHub. We use Singularity to execute containers on the HPC system.

Each container is first downloaded and stored in .simg format to maximise time efficiency. We suggest creating a folder containing all containers in .simg format close to your root directory and adding the path to the folder to the process_one_set.sh pipeline scripts.

To create a .simg file you will require Singularity to be installed and executable, then do:

singularity build <name_of_container>.simg docker://<dockeruser>/<container>:<version>

For Example:

singularity build stitch_plots.simg docker://phytooracle/stitch_plots:latest

Full list of containers

StereoTopRGB

Container	DockerHub Repo	GitHub Link
bin2tif	docker://phytooracle/rgb_bin_to_tif:latest	https://github.com/phytooracle/rgb_bin_to_tif
collect_gps	docker://phytooracle/rgb_flir_collect_gps:latest	https://github.com/phytooracle/rgb_flir_collect_gps
Orthomosaicing	docker://ariyanzarei/full_geocorrection:latest	https://github.com/ariyanzri/Lettuce_Image_Stitching
replace_gps	docker://phytooracle/rgb_flir_edit_gps:latest	https://github.com/phytooracle/rgb_flir_edit_gps
plotclip	docker://phytooracle/rgb_flir_plot_clip_geojson:latest	https://github.com/phytooracle/rgb_flir_plot_clip_geojson
Plant detection	docker://phytooracle/rgb_flir_plant_detection	https://github.com/phytooracle/rgb_flir_plant_detection
Plant clustering	docker://phytooracle/rgb_flir_plant_clustering:latest	https://github.com/phytooracle/rgb_flir_plant_clustering

FlirIr

Container	DockerHub Repo	GitHub Link
flir2tif	docker://phytooracle/flir_bin_to_tif_s10:latest	https://github.com/phytooracle/flir_bin_to_tif_s10
collect_gps	docker://phytooracle/rgb_flir_collect_gps:latest	https://github.com/phytooracle/rgb_flir_collect_gps
Orthomosaicing	docker://ariyanzarei/full_geocorrection:latest	https://github.com/ariyanzri/Lettuce_Image_Stitching
replace_gps	docker://phytooracle/rgb_flir_edit_gps:latest	https://github.com/phytooracle/rgb_flir_edit_gps
flir_field_stitch	docker://phytooracle/flir_field_stitch:latest	https://github.com/phytooracle/flir_field_stitch
plotclip	docker://phytooracle/rgb_flir_plot_clip_geojson:latest	https://github.com/phytooracle/rgb_flir_plot_clip_geojson
flir_meantemp	docker://phytooracle/flir_meantemp:latest	https://github.com/phytooracle/flir_meantemp

PSII

Container	DockerHub Repo	GitHub Link
cleanmetadata	docker://AgPipeline/moving-transformer-cleanmetadata:latest	https://github.com/AgPipeline/moving-transformer-cleanmetadata
bin2tif	docker://phytooracle/psii_bin_to_tif:latest	https://github.com/phytooracle/psii_bin_to_tif
resizetif	docker://phytooracle/psii_resize_tif:latest	https://github.com/phytooracle/psii_resize_tif
flir_field_stitch	docker://phytooracle/flir_field_stitch:latest	https://github.com/phytooracle/flir_field_stitch
plotclip	docker://phytooracle/rgb_flir_plot_clip_geojson:latest	https://github.com/phytooracle/rgb_flir_plot_clip_geojson
psii_segmentation	docker://phytooracle/psii_segmentation:latest	https://github.com/phytooracle/psii_segmentation
psii_fluorescence_aggregation	docker://phytooracle/psii_fluorescence_aggregation:latest	https://github.com/phytooracle/psii_fluorescence_aggregation

Scanner3DTop

Container	DockerHub Repo	GitHub Link
3D MergePly	docker://phytooracle/3d_merge_ply:latest	https://github.com/phytooracle/3d_merge_ply