openalea / phenotrack3d Goto Github PK

Phenotyping Maize over time

License: Other

Python 100.00%

maize openalea organs phenotyping tracking

phenotrack3d's Introduction

PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

PhenoTrack3D can be used to track leaf organs over time, in a time-series of 3D maize plant reconstructions. Such 3D reconstructions can be obtained from sets of RGB images with the Phenomenal pipeline (https://github.com/openalea/phenomenal)

Maintainers

Daviet Benoit ([email protected])
Fournier Christian ([email protected])
Pradal Christophe ([email protected])

License

Our code is released under Cecill-C (https://cecill.info/licences/Licence_CeCILL_V1.1-US.txt) licence. See LICENSE file for details.

Install

install dependencies with conda:

conda create -n phenotrack -c conda-forge -c openalea3 openalea.phenomenal skan=0.9
conda activate phenotrack

Clone repo and run setup

git clone https://github.com/openalea/phenotrack3d.git
cd phenotrack3d

References

If you use PhenoTrack3D to your research, cite:

Daviet, B., Fernandez, R., Cabrera-Bosquet, L. et al. PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time. Plant Methods 18, 130 (2022). https://doi.org/10.1186/s13007-022-00961-4

@article {daviet22,
	author = {Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c c} and Pradal, Christophe and Fournier, Christian},
	title = {PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
	elocation-id = @article{daviet2022phenotrack3d,
	title={PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
	author={Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c{c}} and Pradal, Christophe and Fournier, Christian},
	journal={Plant Methods},
	volume={18},
	number={1},
	pages={1--14},
	year={2022},
	publisher={Springer}
}

phenotrack3d's People

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pradal rocsg

phenotrack3d's Issues

PackagesNotFoundError: - openalea.phenomenal

Hi,
Romain suggested me to try this package. I would be appreicated if you can help me with the installation.

I have tried to create the conda environment based on
conda create -n phenotrack -c conda-forge -c openalea3 openalea.phenomenal skan=0.9
And I got

`Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

openalea.phenomenal

Current channels:

https://conda.anaconda.org/conda-forge/win-64

https://conda.anaconda.org/conda-forge/noarch

https://conda.anaconda.org/openalea3/win-64

https://conda.anaconda.org/openalea3/noarch

https://repo.anaconda.com/pkgs/main/win-64

https://repo.anaconda.com/pkgs/main/noarch

https://repo.anaconda.com/pkgs/r/win-64

https://repo.anaconda.com/pkgs/r/noarch

https://repo.anaconda.com/pkgs/msys2/win-64

https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.`

Any thought?
Thank you in advance.
Best,
Tien-Cheng

Add Citation.cff and connect repository to Zenodo

Add Citation.cff file format.
This will allow to automatically keep the citation (author,name, ..) when uploading to zenodo.
The file can be generated with cffinit website.
More information can be found here

Conda packaging and CI

Create a conda package
Update it automatically on openalea3 channel using Github Continuous Integration

ModuleNotFoundError: No module named 'openalea.maizetrack'

Hi,

When I try
(phenotrack) C:\Users\twang\phenotrack3d\examples>python tutorial_leaf_extension.py
I got
ModuleNotFoundError: No module named 'openalea.maizetrack'
I can see maizetrack.py is in the folder of src in this repository but still failed to import.

Any clue?
Thanks.
Tien

TypeError: leaf_extension() got an unexpected keyword argument 'display_angle'

Hi,
I got new error from
(phm) C:\Users\twang\phenotrack3d>python examples/tutorial_leaf_extension.py

Traceback (most recent call last):
  File "examples/tutorial_leaf_extension.py", line 28, in <module>
TypeError: leaf_extension() got an unexpected keyword argument 'display_angle'

ModuleNotFoundError: No module named 'alinea'

Hi,

When I try
(phenotrack) C:\Users\HAIER\phenotrack3d\examples>python tutorial_leaf_extension.py
I got
ModuleNotFoundError: No module named 'alinea'
I can see maizetrack.py is in the folder of src in this repository but still failed to import.

Thanks.