Extract traits using DicotPipeline

[linwang9926]

Error when extracting traits for canola and soybean.
Error message: GEOSException: IllegalArgumentException: point array must contain 0 or >1 elements

Code to reproduce the error:

import sleap_roots as sr
import os

###### TODO: change the final_datasets folder #####
os.chdir("C:/Work/4_Plant_Phenomics_SLEAP/6_SLEAP_github/final_datasets") 
#%% canola
data_folders = """
Canola_subset/subset_h5files_predictions_proofread
""".strip().split()

# Primary root prediction file ending: {barcode}.{primary_name}.predictions.slp 
primary_name = "primary_multi_day"
# Lateral root prediction file ending: {barcode}.{lateral_name}.predictions.slp 
lateral_name = "lateral_3_nodes"
# When `write_csv = True` a csv with the root traits will be saved at the `csv_path`
write_csv = True
dir_name = "./Canola_subset"
csv_path = f"{dir_name}/canola_subset_proofread_traits.csv"

# Each series is expected to have 72 images. Series with a different number of frames will be excluded from the analysis.
n_imgs_expected = 72

# Find all of the plants in the `data_folders`
plants = sr.find_all_series(data_folders)

# Load series
all_series = [sr.Series.load(p, primary_name=primary_name, lateral_name=lateral_name) for p in plants]
print(f"Loaded {len(all_series)} series.")

# Filter by expected images
all_series = [series for series in all_series if len(series) == n_imgs_expected]
print(f"Kept {len(all_series)} series after filtering by number of images ({n_imgs_expected} expected).")

# Compute the traits using the `DicotPipeline`
pipeline = sr.DicotPipeline()
# Dataframe with summary statistics of root traits for all of the plants found in the `data_folders`
all_traits_df = pipeline.compute_batch_traits(all_series, write_csv=write_csv, csv_path=csv_path)

Detailed information on the error:
"
Cell In[55], line 1
all_traits_df = pipeline.compute_batch_traits(all_series, write_csv=write_csv, csv_path=csv_path)

File C:\Work\4_Plant_Phenomics_SLEAP\6_SLEAP_github\sleap-roots\sleap_roots\trait_pipelines.py:361 in compute_batch_traits
plant_traits = self.compute_plant_traits(plant)

File C:\Work\4_Plant_Phenomics_SLEAP\6_SLEAP_github\sleap-roots\sleap_roots\trait_pipelines.py:306 in compute_plant_traits
frame_traits = self.compute_frame_traits(initial_traits)

File C:\Work\4_Plant_Phenomics_SLEAP\6_SLEAP_github\sleap-roots\sleap_roots\trait_pipelines.py:254 in compute_frame_traits
traits[trait_name] = trait_def.fn(

File C:\Work\4_Plant_Phenomics_SLEAP\6_SLEAP_github\sleap-roots\sleap_roots\networklength.py:201 in get_network_distribution
root_poly = LineString(root)

File ~\Anaconda3\envs\sleap_roots_v0922\lib\site-packages\shapely\geometry\linestring.py:73 in new
geom = shapely.linestrings(coordinates)

File ~\Anaconda3\envs\sleap_roots_v0922\lib\site-packages\shapely\decorators.py:77 in wrapped
return func(*args, **kwargs)

File ~\Anaconda3\envs\sleap_roots_v0922\lib\site-packages\shapely\creation.py:120 in linestrings
return lib.linestrings(coords, out=out, **kwargs)

GEOSException: IllegalArgumentException: point array must contain 0 or >1 elements
"