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 |