The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems
The ClusterGrowth functionality does not work. It just throws an error because it still wants to use an old version of the field cluster detection.
Code for reproduction:
from amep import load
from amep.evaluate import ClusterGrowth
f_traj = load.traj(<Field_trajectory_path>)
ClusterGrowth(
Error message:
Traceback (most recent call last):
File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 146, in
gen_growth_data(field_trajectories)
File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 72, in gen_growth_data
wmea_c_grow = np.stack([ClusterGrowth(trajec,
^^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 72, in
wmea_c_grow = np.stack([ClusterGrowth(trajec,
^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/evaluate.py", line 3538, in init
self.frames, self.avg, self.__indices = average_func(
^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/utils.py", line 141, in average_func
func_result = [func(x, kwargs) for x in tqdm(data[evaluated_indices])]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/utils.py", line 141, in
func_result = [func(x, kwargs) for x in tqdm(data[evaluated_indices])]
^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/evaluate.py", line 3612, in __compute_fields
ids, labels = identify_clusters(
^^^^^^^^^^^^^^^^^^
TypeError: identify_clusters() got an unexpected keyword argument 'field'
Python and AMEP versions:
Python 3.11.9
AMEP 1.0.0
Additional information:
I won't add all the reproducabillity etc. since I'll fix it myself.
Description:
The
ClusterGrowth
functionality does not work. It just throws an error because it still wants to use an old version of the field cluster detection.Code for reproduction:
Error message:
Traceback (most recent call last): File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 146, in
gen_growth_data(field_trajectories)
File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 72, in gen_growth_data
wmea_c_grow = np.stack([ClusterGrowth(trajec,
^^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep_data/amep_publication_plots/gen_cluster_data.py", line 72, in
wmea_c_grow = np.stack([ClusterGrowth(trajec,
^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/evaluate.py", line 3538, in init
self.frames, self.avg, self.__indices = average_func(
^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/utils.py", line 141, in average_func
func_result = [func(x, kwargs) for x in tqdm(data[evaluated_indices])]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/utils.py", line 141, in
func_result = [func(x, kwargs) for x in tqdm(data[evaluated_indices])]
^^^^^^^^^^^^^^^^^
File "/home/kspanheimer/Documents/dev/amep_project/amep/amep/evaluate.py", line 3612, in __compute_fields
ids, labels = identify_clusters(
^^^^^^^^^^^^^^^^^^
TypeError: identify_clusters() got an unexpected keyword argument 'field'
Python and AMEP versions:
Python 3.11.9 AMEP 1.0.0
Additional information:
I won't add all the reproducabillity etc. since I'll fix it myself.
How did you install AMEP?
pip