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kapoorlab committed Jan 23, 2024
1 parent 4ba52d8 commit 1eaa6cc
Showing 1 changed file with 4 additions and 89 deletions.
93 changes: 4 additions & 89 deletions src/napatrackmater/Trackvector.py
Original file line number Diff line number Diff line change
Expand Up @@ -1544,49 +1544,7 @@ def simple_unsupervised_clustering(
+ f"_wcss_{metric}_{cluster_threshold}.npy"
)
np.save(wcss_file_name, wcss_value)
track_id_to_cluster = {
track_id: cluster_label
for track_id, cluster_label in zip(
analysis_track_ids, shape_dynamic_cluster_labels
)
}
full_dataframe["Cluster"] = full_dataframe["Track ID"].map(
track_id_to_cluster
)
result_dataframe = full_dataframe[
["Track ID", "t", "z", "y", "x", "Cluster"]
]
csv_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ ".csv"
)

if os.path.exists(csv_file_name):
os.remove(csv_file_name)
result_dataframe.to_csv(csv_file_name, index=False)

mean_matrix_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_covariance.npy"
)
np.save(mean_matrix_file_name, track_arrays)

linkage_npy_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_linkage.npy"
)
np.save(linkage_npy_file_name, shape_dynamic_linkage_matrix)

cluster_labels_npy_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_cluster_labels.npy"
)
np.save(cluster_labels_npy_file_name, shape_dynamic_cluster_labels)



def unsupervised_clustering(
full_dataframe,
Expand Down Expand Up @@ -1729,62 +1687,19 @@ def unsupervised_clustering(
+ f"_wcss_{metric}_{cluster_threshold}.npy"
)
np.save(wcss_file_name, wcss_value)
track_id_to_cluster = {
track_id: cluster_label
for track_id, cluster_label in zip(
analysis_track_ids, shape_dynamic_cluster_labels
)
}
full_dataframe["Cluster"] = full_dataframe["Track ID"].map(
track_id_to_cluster
)
result_dataframe = full_dataframe[
["Track ID", "t", "z", "y", "x", "Cluster"]
]
csv_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ ".csv"
)

if os.path.exists(csv_file_name):
os.remove(csv_file_name)
result_dataframe.to_csv(csv_file_name, index=False)


mean_matrix_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_covariance.npy"
)
np.save(mean_matrix_file_name, track_arrays)

linkage_npy_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_linkage.npy"
)
np.save(linkage_npy_file_name, shape_dynamic_linkage_matrix)

cluster_labels_npy_file_name = (
csv_file_name_original
+ track_arrays_array_names[track_arrays_array.index(track_arrays)]
+ f"_{metric}_cluster_labels.npy"
)
np.save(cluster_labels_npy_file_name, shape_dynamic_cluster_labels)



def convert_tracks_to_arrays(
analysis_vectors,
min_length=None,
metric="euclidean",
cluster_threshold_shape_dynamic=4,
cluster_threshold_dynamic=4,
cluster_threshold_shape=4,
method="ward",
criterion="maxclust",
starting_label_shape_dynamic=0,
starting_label_dynamic=0,
starting_label_shape=0,

):

analysis_track_ids = []
Expand Down

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