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a/lightning_logs/version_91/events.out.tfevents.1697383476.Kapoorlabs.20628.91 b/lightning_logs/version_91/events.out.tfevents.1697383476.Kapoorlabs.20628.91 new file mode 100644 index 00000000..8bfd8b5f Binary files /dev/null and b/lightning_logs/version_91/events.out.tfevents.1697383476.Kapoorlabs.20628.91 differ diff --git a/lightning_logs/version_91/hparams.yaml b/lightning_logs/version_91/hparams.yaml new file mode 100644 index 00000000..0f6bf15c --- /dev/null +++ b/lightning_logs/version_91/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/lightning_logs/version_92/events.out.tfevents.1697383540.Kapoorlabs.20628.92 b/lightning_logs/version_92/events.out.tfevents.1697383540.Kapoorlabs.20628.92 new file mode 100644 index 00000000..2faa4ebe Binary files /dev/null and b/lightning_logs/version_92/events.out.tfevents.1697383540.Kapoorlabs.20628.92 differ diff --git a/lightning_logs/version_92/hparams.yaml b/lightning_logs/version_92/hparams.yaml new file mode 100644 index 00000000..0f6bf15c --- /dev/null +++ b/lightning_logs/version_92/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/lightning_logs/version_93/events.out.tfevents.1697383565.Kapoorlabs.20628.93 b/lightning_logs/version_93/events.out.tfevents.1697383565.Kapoorlabs.20628.93 new file mode 100644 index 00000000..4ad193a0 Binary files /dev/null and b/lightning_logs/version_93/events.out.tfevents.1697383565.Kapoorlabs.20628.93 differ diff --git a/lightning_logs/version_93/hparams.yaml b/lightning_logs/version_93/hparams.yaml new file mode 100644 index 00000000..0f6bf15c --- /dev/null +++ b/lightning_logs/version_93/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/lightning_logs/version_94/events.out.tfevents.1697383624.Kapoorlabs.20628.94 b/lightning_logs/version_94/events.out.tfevents.1697383624.Kapoorlabs.20628.94 new file mode 100644 index 00000000..6e645cce Binary files /dev/null and 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b/lightning_logs/version_97/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/lightning_logs/version_98/events.out.tfevents.1697383889.Kapoorlabs.20628.98 b/lightning_logs/version_98/events.out.tfevents.1697383889.Kapoorlabs.20628.98 new file mode 100644 index 00000000..c2745b20 Binary files /dev/null and b/lightning_logs/version_98/events.out.tfevents.1697383889.Kapoorlabs.20628.98 differ diff --git a/lightning_logs/version_98/hparams.yaml b/lightning_logs/version_98/hparams.yaml new file mode 100644 index 00000000..0f6bf15c --- /dev/null +++ b/lightning_logs/version_98/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/lightning_logs/version_99/events.out.tfevents.1697383954.Kapoorlabs.20628.99 b/lightning_logs/version_99/events.out.tfevents.1697383954.Kapoorlabs.20628.99 new file mode 100644 index 00000000..e1186676 Binary files /dev/null and b/lightning_logs/version_99/events.out.tfevents.1697383954.Kapoorlabs.20628.99 differ diff --git a/lightning_logs/version_99/hparams.yaml b/lightning_logs/version_99/hparams.yaml new file mode 100644 index 00000000..0f6bf15c --- /dev/null +++ b/lightning_logs/version_99/hparams.yaml @@ -0,0 +1,2 @@ +scale_z: 8 +scale_xy: 16 diff --git a/src/napatrackmater/Trackmate.py b/src/napatrackmater/Trackmate.py index 797ebc57..06736f53 100644 --- a/src/napatrackmater/Trackmate.py +++ b/src/napatrackmater/Trackmate.py @@ -43,6 +43,7 @@ def __init__( autoencoder_model=None, num_points=2048, batch_size=1, + compute_with_autoencoder=True, ): self.xml_path = xml_path @@ -55,6 +56,7 @@ def __init__( self.scale_z = scale_z self.scale_xy = scale_xy self.center = center + self.compute_with_autoencoder = compute_with_autoencoder if image is not None: self.image = image.astype(np.uint8) else: @@ -1668,6 +1670,7 @@ def _assign_cluster_class(self): scale_z=self.scale_z, scale_xy=self.scale_xy, center=self.center, + compute_with_autoencoder=self.compute_with_autoencoder, ) cluster_eval._create_cluster_labels() diff --git a/src/napatrackmater/_version.py b/src/napatrackmater/_version.py index bbc9e04a..4330d66e 100644 --- a/src/napatrackmater/_version.py +++ b/src/napatrackmater/_version.py @@ -1,2 +1,2 @@ -__version__ = version = "4.2.8" -__version_tuple__ = version_tuple = (4, 2, 8) +__version__ = version = "4.2.9" +__version_tuple__ = version_tuple = (4, 2, 9) diff --git a/src/napatrackmater/clustering.py b/src/napatrackmater/clustering.py index 22b29163..3863e175 100644 --- a/src/napatrackmater/clustering.py +++ b/src/napatrackmater/clustering.py @@ -13,6 +13,7 @@ from scipy.spatial import ConvexHull from lightning import Trainer from typing import List +from tqdm import tqdm class PointCloudDataset(Dataset): @@ -56,6 +57,7 @@ def __init__( scale_z=1.0, scale_xy=1.0, center=True, + compute_with_autoencoder=True, ): self.accelerator = accelerator @@ -71,6 +73,7 @@ def __init__( self.progress_bar = progress_bar self.key = key self.batch_size = batch_size + self.compute_with_autoencoder = compute_with_autoencoder self.timed_cluster_label = {} self.count = 0 @@ -100,6 +103,7 @@ def _create_cluster_labels(self): clouds, labels, centroids, + self.compute_with_autoencoder, self.batch_size, self.scale_z, self.scale_xy, @@ -137,6 +141,7 @@ def _create_cluster_labels(self): clouds, labels, centroids, + self.compute_with_autoencoder, self.batch_size, self.scale_z, self.scale_xy, @@ -222,6 +227,7 @@ def _label_computer(self, i, dim): clouds, labels, centroids, + self.compute_with_autoencoder, self.batch_size, self.scale_z, self.scale_xy, @@ -245,6 +251,7 @@ def _model_output( clouds, labels, centroids, + compute_with_autoencoder, batch_size: int, scale_z: float = 1.0, scale_xy: float = 1.0, @@ -259,35 +266,66 @@ def _model_output( output_dimensions = [] dataset = PointCloudDataset(clouds, scale_z=scale_z, scale_xy=scale_xy) dataloader = DataLoader(dataset, batch_size=batch_size) - model.eval() - print(f"Predicting {len(dataset)} clouds..., {len(centroids)} centroids...") - pretrainer = Trainer(accelerator=accelerator, devices=devices) - outputs_list = pretrainer.predict(model=model, dataloaders=dataloader) - output_cluster_centroid = output_cluster_centroid + [ - tuple(centroid_input) for centroid_input in centroids - ] - output_labels = output_labels + [int(float(label_input)) for label_input in labels] - for outputs in outputs_list: - output_cloud_eccentricity = output_cloud_eccentricity + [ - tuple(get_eccentricity(cloud_input.detach().cpu().numpy()))[0] - for cloud_input in outputs + if compute_with_autoencoder: + + model.eval() + print(f"Predicting {len(dataset)} clouds..., {len(centroids)} centroids...") + pretrainer = Trainer(accelerator=accelerator, devices=devices) + outputs_list = pretrainer.predict(model=model, dataloaders=dataloader) + output_cluster_centroid = output_cluster_centroid + [ + tuple(centroid_input) for centroid_input in centroids ] - output_largest_eigenvector = output_largest_eigenvector + [ - get_eccentricity(cloud_input.detach().cpu().numpy())[1] - for cloud_input in outputs - ] - output_largest_eigenvalue = output_largest_eigenvalue + [ - get_eccentricity(cloud_input.detach().cpu().numpy())[2] - for cloud_input in outputs - ] - output_dimensions = output_dimensions + [ - get_eccentricity(cloud_input.detach().cpu().numpy())[3] - for cloud_input in outputs - ] - output_cloud_surface_area = output_cloud_surface_area + [ - float(get_surface_area(cloud_input.detach().cpu().numpy())) - for cloud_input in outputs + output_labels = output_labels + [ + int(float(label_input)) for label_input in labels ] + for outputs in outputs_list: + output_cloud_eccentricity = output_cloud_eccentricity + [ + tuple(get_eccentricity(cloud_input.detach().cpu().numpy()))[0] + for cloud_input in outputs + ] + output_largest_eigenvector = output_largest_eigenvector + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[1] + for cloud_input in outputs + ] + output_largest_eigenvalue = output_largest_eigenvalue + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[2] + for cloud_input in outputs + ] + output_dimensions = output_dimensions + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[3] + for cloud_input in outputs + ] + output_cloud_surface_area = output_cloud_surface_area + [ + float(get_surface_area(cloud_input.detach().cpu().numpy())) + for cloud_input in outputs + ] + + else: + + print("Computing shape features using classical marching cubes ") + for data in tqdm(dataloader): + + cloud_inputs, label_inputs, centroid_inputs = data + output_cloud_eccentricity = output_cloud_eccentricity + [ + tuple(get_eccentricity(cloud_input.detach().cpu().numpy()))[0] + for cloud_input in cloud_inputs + ] + output_largest_eigenvector = output_largest_eigenvector + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[1] + for cloud_input in cloud_inputs + ] + output_largest_eigenvalue = output_largest_eigenvalue + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[2] + for cloud_input in cloud_inputs + ] + output_dimensions = output_dimensions + [ + get_eccentricity(cloud_input.detach().cpu().numpy())[3] + for cloud_input in cloud_inputs + ] + output_cloud_surface_area = output_cloud_surface_area + [ + float(get_surface_area(cloud_input.detach().cpu().numpy())) + for cloud_input in cloud_inputs + ] return ( output_labels,