From c81d2b0b33d5df665df895a6a4b01591eb0a6678 Mon Sep 17 00:00:00 2001 From: Constantin Pape Date: Fri, 6 Dec 2024 19:50:25 +0100 Subject: [PATCH] Rename library in all experiment scripts --- .github/workflows/build_docs.yaml | 2 +- build_doc.py | 2 +- examples/domain_adaptation.py | 4 ++-- examples/network_training.py | 2 +- scripts/cooper/analysis/active_zone_analysis.py | 6 +++--- scripts/cooper/analysis/check_size_export.py | 2 +- scripts/cooper/analysis/export_az_to_imod.py | 2 +- scripts/cooper/analysis/export_vesicles_to_imod.py | 2 +- scripts/cooper/analysis/measure_distances.py | 2 +- scripts/cooper/analysis/measure_vesicle_sizes.py | 2 +- scripts/cooper/analysis/proofread_bad_azs.py | 4 ++-- scripts/cooper/export_mask_to_imod.py | 2 +- scripts/cooper/export_vesicles_to_imod.py | 2 +- scripts/cooper/extract_mask_from_imod.py | 2 +- .../cooper/full_reconstruction/segment_compartments.py | 2 +- .../cooper/full_reconstruction/segment_mitochondria.py | 2 +- .../cooper/ground_truth/2D-data/extract_vesicles.py | 2 +- scripts/cooper/ground_truth/az/proofread_az.py | 4 ++-- .../ground_truth/compartments/check_predictions.py | 2 +- .../ground_truth/compartments/export_compartment_gt.py | 2 +- .../ground_truth/compartments/run_prediction_04.py | 4 ++-- .../cooper/ground_truth/explore_imod_annotations.py | 2 +- .../cooper/ground_truth/vesicles/compare_version.py | 2 +- .../cooper/ground_truth/vesicles/vesicle_extraction.py | 2 +- .../ground_truth/vesicles/vesicle_postprocessing.py | 10 +++++----- scripts/cooper/run_compartment_segmentation.py | 4 ++-- scripts/cooper/run_cristae_segmentation.py | 4 ++-- scripts/cooper/run_mitochondria_segmentation.py | 4 ++-- scripts/cooper/run_vesicle_segmentation.py | 4 ++-- scripts/cooper/training/train_AZ.py | 8 ++++---- scripts/cooper/training/train_compartments.py | 2 +- scripts/cooper/training/train_vesicles.py | 8 ++++---- scripts/cooper/vesicle_segmentation_h5.py | 4 ++-- scripts/cryo/actin/predict_actin.py | 2 +- scripts/cryo/actin/train_actin_segmentation.py | 2 +- scripts/cryo/actin/train_domain_adaptation.py | 2 +- scripts/cryo/vesicles/debug_vesicle_seg.py | 2 +- scripts/cryo/vesicles/train_domain_adaptation.py | 8 ++++---- .../inner_ear/analysis/analyze_vesicle_diameters.py | 4 ++-- scripts/inner_ear/analysis/check_outliers.py | 2 +- scripts/inner_ear/analysis/check_radii.py | 4 ++-- scripts/inner_ear/analysis/export_seg_to_imod.py | 2 +- scripts/inner_ear/check_manual_analysis.py | 4 ++-- scripts/inner_ear/check_results.py | 4 ++-- .../ground_truth/extract_automatic_structures.py | 4 ++-- .../inner_ear/processing/analyze_manual_annotations.py | 2 +- scripts/inner_ear/processing/check_resolutions.py | 2 +- scripts/inner_ear/processing/compute_morphology.py | 4 ++-- .../processing/process_manual_segmentation.py | 4 ++-- scripts/inner_ear/processing/refine_vesicle_shapes.py | 4 ++-- scripts/inner_ear/processing/rescale_tomogram.py | 2 +- scripts/inner_ear/processing/run_analyis.py | 8 ++++---- .../processing/run_structure_postprocessing.py | 4 ++-- .../inner_ear/processing/run_structure_prediction.py | 10 +++++----- .../inner_ear/processing/run_vesicle_segmentation.py | 10 +++++----- .../training/postprocessing_and_evaluation.py | 8 ++++---- .../training/structure_prediction_and_evaluation.py | 4 ++-- scripts/inner_ear/training/train_domain_adaptation.py | 2 +- .../training/train_domain_adaptation_vesicles.py | 8 ++++---- .../inner_ear/training/train_structure_segmentation.py | 2 +- scripts/inner_ear/validate_segmentations.py | 2 +- scripts/inner_ear/vesicle_annotation.py | 2 +- scripts/liposomes/measure_distances.py | 4 ++-- scripts/rizzoli/2D_vesicle_segmentation.py | 4 ++-- .../data_extraction/.gitignore | 0 .../data_extraction/automatic_labeling.py | 0 .../data_extraction/common.py | 0 .../data_extraction/extract_data.py | 0 .../data_extraction/initial_slice_annotation.py | 0 .../data_extraction/train_sam_model.py | 0 scripts/rizzoli/train_2D_domain_adaptation.py | 8 ++++---- scripts/wichmann/export_vesicles_from_imod.py | 2 +- scripts/wichmann/train_domain_adaptation.py | 8 ++++---- test/test_cli.py | 2 +- test/test_distance_measurement.py | 2 +- test/test_file_utils.py | 6 +++--- 76 files changed, 131 insertions(+), 131 deletions(-) rename scripts/{frog_synapses => rizzoli}/data_extraction/.gitignore (100%) rename scripts/{frog_synapses => rizzoli}/data_extraction/automatic_labeling.py (100%) rename scripts/{frog_synapses => rizzoli}/data_extraction/common.py (100%) rename scripts/{frog_synapses => rizzoli}/data_extraction/extract_data.py (100%) rename scripts/{frog_synapses => rizzoli}/data_extraction/initial_slice_annotation.py (100%) rename scripts/{frog_synapses => rizzoli}/data_extraction/train_sam_model.py (100%) diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml index a9ccefd..4f64156 100644 --- a/.github/workflows/build_docs.yaml +++ b/.github/workflows/build_docs.yaml @@ -38,7 +38,7 @@ jobs: - name: Generate Documentation shell: bash -l {0} - run: pdoc synaptic_reconstruction -d google -o doc/ + run: pdoc synapse_net -d google -o doc/ - name: Verify Documentation Output run: ls -la doc/ diff --git a/build_doc.py b/build_doc.py index d4a3cfc..dc30132 100644 --- a/build_doc.py +++ b/build_doc.py @@ -11,6 +11,6 @@ if args.out: cmd.extend(["--out", "tmp/"]) - cmd.append("synaptic_reconstruction") + cmd.append("synapse_net") run(cmd) diff --git a/examples/domain_adaptation.py b/examples/domain_adaptation.py index 8027a5e..afad37c 100644 --- a/examples/domain_adaptation.py +++ b/examples/domain_adaptation.py @@ -13,8 +13,8 @@ from glob import glob from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training import mean_teacher_adaptation -from synaptic_reconstruction.tools.util import get_model_path +from synapse_net.training import mean_teacher_adaptation +from synapse_net.tools.util import get_model_path def main(): diff --git a/examples/network_training.py b/examples/network_training.py index 5d34e36..c90d592 100644 --- a/examples/network_training.py +++ b/examples/network_training.py @@ -12,7 +12,7 @@ from glob import glob from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training import supervised_training +from synapse_net.training import supervised_training def main(): diff --git a/scripts/cooper/analysis/active_zone_analysis.py b/scripts/cooper/analysis/active_zone_analysis.py index bb13ac5..c0a29f1 100644 --- a/scripts/cooper/analysis/active_zone_analysis.py +++ b/scripts/cooper/analysis/active_zone_analysis.py @@ -8,9 +8,9 @@ from scipy.ndimage import binary_closing from skimage.measure import label -from synaptic_reconstruction.ground_truth.shape_refinement import edge_filter -from synaptic_reconstruction.morphology import skeletonize_object -from synaptic_reconstruction.distance_measurements import measure_segmentation_to_object_distances +from synapse_net.ground_truth.shape_refinement import edge_filter +from synapse_net.morphology import skeletonize_object +from synapse_net.distance_measurements import measure_segmentation_to_object_distances from tqdm import tqdm from compute_skeleton_area import calculate_surface_area diff --git a/scripts/cooper/analysis/check_size_export.py b/scripts/cooper/analysis/check_size_export.py index b00fdfa..ea11ae0 100644 --- a/scripts/cooper/analysis/check_size_export.py +++ b/scripts/cooper/analysis/check_size_export.py @@ -2,7 +2,7 @@ def test_export(): - from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod_as_points + from synapse_net.imod.to_imod import write_segmentation_to_imod_as_points from subprocess import run mrc_path = "20241108_3D_Imig_DATA_2014/!_M13DKO_TOMO_DATA_Imig2014_mrc-mod-FM/A_M13DKO_080212_CTRL4.8_crop/A_M13DKO_080212_CTRL4.8_crop.mrc" # noqa diff --git a/scripts/cooper/analysis/export_az_to_imod.py b/scripts/cooper/analysis/export_az_to_imod.py index fe72f01..6950367 100644 --- a/scripts/cooper/analysis/export_az_to_imod.py +++ b/scripts/cooper/analysis/export_az_to_imod.py @@ -7,7 +7,7 @@ import h5py import pandas as pd -from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod +from synapse_net.imod.to_imod import write_segmentation_to_imod from scipy.ndimage import binary_dilation, binary_closing diff --git a/scripts/cooper/analysis/export_vesicles_to_imod.py b/scripts/cooper/analysis/export_vesicles_to_imod.py index d2fe801..47f5441 100644 --- a/scripts/cooper/analysis/export_vesicles_to_imod.py +++ b/scripts/cooper/analysis/export_vesicles_to_imod.py @@ -3,7 +3,7 @@ import h5py -from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod_as_points +from synapse_net.imod.to_imod import write_segmentation_to_imod_as_points def export_all_to_imod(check_input=True, check_export=True): diff --git a/scripts/cooper/analysis/measure_distances.py b/scripts/cooper/analysis/measure_distances.py index e5373c3..0b5adbe 100644 --- a/scripts/cooper/analysis/measure_distances.py +++ b/scripts/cooper/analysis/measure_distances.py @@ -5,7 +5,7 @@ import pandas as pd from tqdm import tqdm -from synaptic_reconstruction.distance_measurements import measure_segmentation_to_object_distances +from synapse_net.distance_measurements import measure_segmentation_to_object_distances RESOLUTION = (1.554,) * 3 diff --git a/scripts/cooper/analysis/measure_vesicle_sizes.py b/scripts/cooper/analysis/measure_vesicle_sizes.py index c4dc5e7..c89c296 100644 --- a/scripts/cooper/analysis/measure_vesicle_sizes.py +++ b/scripts/cooper/analysis/measure_vesicle_sizes.py @@ -5,7 +5,7 @@ import pandas as pd from tqdm import tqdm -from synaptic_reconstruction.imod.to_imod import convert_segmentation_to_spheres +from synapse_net.imod.to_imod import convert_segmentation_to_spheres RESOLUTION = (1.554,) * 3 diff --git a/scripts/cooper/analysis/proofread_bad_azs.py b/scripts/cooper/analysis/proofread_bad_azs.py index e23b068..0ec6cc4 100644 --- a/scripts/cooper/analysis/proofread_bad_azs.py +++ b/scripts/cooper/analysis/proofread_bad_azs.py @@ -8,8 +8,8 @@ from magicgui import magicgui from tqdm import tqdm -from synaptic_reconstruction.morphology import skeletonize_object -from synaptic_reconstruction.ground_truth.shape_refinement import edge_filter +from synapse_net.morphology import skeletonize_object +from synapse_net.ground_truth.shape_refinement import edge_filter def proofread_az(raw_path, seg_path): diff --git a/scripts/cooper/export_mask_to_imod.py b/scripts/cooper/export_mask_to_imod.py index 4273707..b0875e1 100644 --- a/scripts/cooper/export_mask_to_imod.py +++ b/scripts/cooper/export_mask_to_imod.py @@ -1,6 +1,6 @@ import argparse -from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod +from synapse_net.imod.to_imod import write_segmentation_to_imod def export_mask_to_imod(args): diff --git a/scripts/cooper/export_vesicles_to_imod.py b/scripts/cooper/export_vesicles_to_imod.py index dc323c7..6db81e0 100644 --- a/scripts/cooper/export_vesicles_to_imod.py +++ b/scripts/cooper/export_vesicles_to_imod.py @@ -1,7 +1,7 @@ import argparse from functools import partial -from synaptic_reconstruction.imod.to_imod import export_helper, write_segmentation_to_imod_as_points +from synapse_net.imod.to_imod import export_helper, write_segmentation_to_imod_as_points def export_vesicles_to_imod(args): diff --git a/scripts/cooper/extract_mask_from_imod.py b/scripts/cooper/extract_mask_from_imod.py index 75f8e62..80e0ca8 100644 --- a/scripts/cooper/extract_mask_from_imod.py +++ b/scripts/cooper/extract_mask_from_imod.py @@ -2,7 +2,7 @@ import os from pathlib import Path -from synaptic_reconstruction.imod.export import get_label_names, export_segmentation +from synapse_net.imod.export import get_label_names, export_segmentation def extract_mask_from_imod(input_path, mod_file, name, output_folder, interpolation): diff --git a/scripts/cooper/full_reconstruction/segment_compartments.py b/scripts/cooper/full_reconstruction/segment_compartments.py index 6254bc1..2758488 100644 --- a/scripts/cooper/full_reconstruction/segment_compartments.py +++ b/scripts/cooper/full_reconstruction/segment_compartments.py @@ -2,7 +2,7 @@ from glob import glob import h5py -from synaptic_reconstruction.inference.compartments import segment_compartments +from synapse_net.inference.compartments import segment_compartments from tqdm import tqdm ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/04_full_reconstruction" # noqa diff --git a/scripts/cooper/full_reconstruction/segment_mitochondria.py b/scripts/cooper/full_reconstruction/segment_mitochondria.py index cb82275..1a35d1c 100644 --- a/scripts/cooper/full_reconstruction/segment_mitochondria.py +++ b/scripts/cooper/full_reconstruction/segment_mitochondria.py @@ -2,7 +2,7 @@ from glob import glob import h5py -from synaptic_reconstruction.inference.mitochondria import segment_mitochondria +from synapse_net.inference.mitochondria import segment_mitochondria from tqdm import tqdm ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/04_full_reconstruction" # noqa diff --git a/scripts/cooper/ground_truth/2D-data/extract_vesicles.py b/scripts/cooper/ground_truth/2D-data/extract_vesicles.py index 398c513..4a6223d 100644 --- a/scripts/cooper/ground_truth/2D-data/extract_vesicles.py +++ b/scripts/cooper/ground_truth/2D-data/extract_vesicles.py @@ -6,7 +6,7 @@ import numpy as np from elf.io import open_file from magicgui import magicgui -from synaptic_reconstruction.imod.export import export_point_annotations +from synapse_net.imod.export import export_point_annotations EXPORT_FOLDER = "./exported" diff --git a/scripts/cooper/ground_truth/az/proofread_az.py b/scripts/cooper/ground_truth/az/proofread_az.py index 5522ff2..febcd1a 100644 --- a/scripts/cooper/ground_truth/az/proofread_az.py +++ b/scripts/cooper/ground_truth/az/proofread_az.py @@ -8,8 +8,8 @@ from magicgui import magicgui from scipy.ndimage import binary_dilation, binary_closing -from synaptic_reconstruction.morphology import skeletonize_object -from synaptic_reconstruction.ground_truth.shape_refinement import edge_filter +from synapse_net.morphology import skeletonize_object +from synapse_net.ground_truth.shape_refinement import edge_filter def proofread_az(raw_path, seg_path): diff --git a/scripts/cooper/ground_truth/compartments/check_predictions.py b/scripts/cooper/ground_truth/compartments/check_predictions.py index a02b1da..5c72cc6 100644 --- a/scripts/cooper/ground_truth/compartments/check_predictions.py +++ b/scripts/cooper/ground_truth/compartments/check_predictions.py @@ -4,7 +4,7 @@ import h5py import napari -from synaptic_reconstruction.inference.compartments import _segment_compartments_3d +from synapse_net.inference.compartments import _segment_compartments_3d def check_pred(path, pred_path, name): diff --git a/scripts/cooper/ground_truth/compartments/export_compartment_gt.py b/scripts/cooper/ground_truth/compartments/export_compartment_gt.py index 3bba4fa..1a1220b 100644 --- a/scripts/cooper/ground_truth/compartments/export_compartment_gt.py +++ b/scripts/cooper/ground_truth/compartments/export_compartment_gt.py @@ -10,7 +10,7 @@ from skimage.measure import label, regionprops from skimage.morphology import remove_small_holes from skimage.segmentation import watershed -from synaptic_reconstruction.ground_truth.shape_refinement import edge_filter +from synapse_net.ground_truth.shape_refinement import edge_filter from tqdm import tqdm diff --git a/scripts/cooper/ground_truth/compartments/run_prediction_04.py b/scripts/cooper/ground_truth/compartments/run_prediction_04.py index 4e302ae..831b4c3 100644 --- a/scripts/cooper/ground_truth/compartments/run_prediction_04.py +++ b/scripts/cooper/ground_truth/compartments/run_prediction_04.py @@ -4,8 +4,8 @@ import h5py from tqdm import tqdm -from synaptic_reconstruction.inference.util import _Scaler -from synaptic_reconstruction.inference.compartments import segment_compartments +from synapse_net.inference.util import _Scaler +from synapse_net.inference.compartments import segment_compartments INPUT_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/ground_truth/04Dataset_for_vesicle_eval" # noqa # MODEL_PATH = "/mnt/lustre-emmy-hdd/projects/nim00007/compartment_models/compartment_model_3d.pt" diff --git a/scripts/cooper/ground_truth/explore_imod_annotations.py b/scripts/cooper/ground_truth/explore_imod_annotations.py index f67f409..8054c72 100644 --- a/scripts/cooper/ground_truth/explore_imod_annotations.py +++ b/scripts/cooper/ground_truth/explore_imod_annotations.py @@ -4,7 +4,7 @@ from glob import glob import numpy as np -from synaptic_reconstruction.imod import get_label_names +from synapse_net.imod import get_label_names from tqdm import tqdm ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/original_imod_data/20240909_cp_datatransfer" # noqa diff --git a/scripts/cooper/ground_truth/vesicles/compare_version.py b/scripts/cooper/ground_truth/vesicles/compare_version.py index 667c7d6..7734b45 100644 --- a/scripts/cooper/ground_truth/vesicles/compare_version.py +++ b/scripts/cooper/ground_truth/vesicles/compare_version.py @@ -3,7 +3,7 @@ def main(): - root_old = "/scratch-grete/projects/nim00007/data/synaptic_reconstruction/train_data_cooper" + root_old = "/scratch-grete/projects/nim00007/data/synapse_net/train_data_cooper" root_new = "/projects/extern/nhr/nhr_ni/nim00007/dir.project/data/synaptic-reconstruction/cooper/original_imod_data/20240909_cp_datatransfer" # noqa old_folders = sorted(glob(os.path.join(root_old, "0*"))) + sorted(glob(os.path.join(root_old, "1*"))) diff --git a/scripts/cooper/ground_truth/vesicles/vesicle_extraction.py b/scripts/cooper/ground_truth/vesicles/vesicle_extraction.py index 49c1d03..bf6bee0 100644 --- a/scripts/cooper/ground_truth/vesicles/vesicle_extraction.py +++ b/scripts/cooper/ground_truth/vesicles/vesicle_extraction.py @@ -2,7 +2,7 @@ from glob import glob from pathlib import Path -from synaptic_reconstruction.ground_truth import extract_vesicle_training_data +from synapse_net.ground_truth import extract_vesicle_training_data ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/original_imod_data/20240909_cp_datatransfer" # noqa OUT_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/extracted/20240909_cp_datatransfer" # noqa diff --git a/scripts/cooper/ground_truth/vesicles/vesicle_postprocessing.py b/scripts/cooper/ground_truth/vesicles/vesicle_postprocessing.py index be165a1..795df7c 100644 --- a/scripts/cooper/ground_truth/vesicles/vesicle_postprocessing.py +++ b/scripts/cooper/ground_truth/vesicles/vesicle_postprocessing.py @@ -9,12 +9,12 @@ from scipy.ndimage import binary_dilation from tqdm import tqdm -from synaptic_reconstruction.inference.vesicles import segment_vesicles -# from synaptic_reconstruction.ground_truth import find_additional_objects -from synaptic_reconstruction.inference.util import _get_file_paths -from synaptic_reconstruction.ground_truth.shape_refinement import refine_vesicle_shapes, edge_filter +from synapse_net.inference.vesicles import segment_vesicles +# from synapse_net.ground_truth import find_additional_objects +from synapse_net.inference.util import _get_file_paths +from synapse_net.ground_truth.shape_refinement import refine_vesicle_shapes, edge_filter -MODEL_PATH = "/scratch-grete/projects/nim00007/data/synaptic_reconstruction/models/cooper/vesicles/3D-UNet-for-Vesicle-Segmentation-vesicles-010508model_v1r45_0105mr45_0105mr45.zip" # noqa +MODEL_PATH = "/scratch-grete/projects/nim00007/data/synapse_net/models/cooper/vesicles/3D-UNet-for-Vesicle-Segmentation-vesicles-010508model_v1r45_0105mr45_0105mr45.zip" # noqa def extract_gt_bounding_box(raw, vesicle_gt, halo=[2, 32, 32]): diff --git a/scripts/cooper/run_compartment_segmentation.py b/scripts/cooper/run_compartment_segmentation.py index 08073b6..0c8e908 100644 --- a/scripts/cooper/run_compartment_segmentation.py +++ b/scripts/cooper/run_compartment_segmentation.py @@ -1,8 +1,8 @@ import argparse from functools import partial -from synaptic_reconstruction.inference.compartments import segment_compartments -from synaptic_reconstruction.inference.util import inference_helper, parse_tiling +from synapse_net.inference.compartments import segment_compartments +from synapse_net.inference.util import inference_helper, parse_tiling def run_compartment_segmentation(args): diff --git a/scripts/cooper/run_cristae_segmentation.py b/scripts/cooper/run_cristae_segmentation.py index 8fa5ace..8b8eb0c 100644 --- a/scripts/cooper/run_cristae_segmentation.py +++ b/scripts/cooper/run_cristae_segmentation.py @@ -1,8 +1,8 @@ import argparse from functools import partial -from synaptic_reconstruction.inference.cristae import segment_cristae -from synaptic_reconstruction.inference.util import inference_helper, parse_tiling +from synapse_net.inference.cristae import segment_cristae +from synapse_net.inference.util import inference_helper, parse_tiling def run_cristae_segmentation(args): diff --git a/scripts/cooper/run_mitochondria_segmentation.py b/scripts/cooper/run_mitochondria_segmentation.py index d800c63..a71af91 100644 --- a/scripts/cooper/run_mitochondria_segmentation.py +++ b/scripts/cooper/run_mitochondria_segmentation.py @@ -1,8 +1,8 @@ import argparse from functools import partial -from synaptic_reconstruction.inference.mitochondria import segment_mitochondria -from synaptic_reconstruction.inference.util import inference_helper, parse_tiling +from synapse_net.inference.mitochondria import segment_mitochondria +from synapse_net.inference.util import inference_helper, parse_tiling def run_mitochondria_segmentation(args): diff --git a/scripts/cooper/run_vesicle_segmentation.py b/scripts/cooper/run_vesicle_segmentation.py index 70401bd..c4b749b 100644 --- a/scripts/cooper/run_vesicle_segmentation.py +++ b/scripts/cooper/run_vesicle_segmentation.py @@ -1,8 +1,8 @@ import argparse from functools import partial -from synaptic_reconstruction.inference.vesicles import segment_vesicles -from synaptic_reconstruction.inference.util import inference_helper, parse_tiling +from synapse_net.inference.vesicles import segment_vesicles +from synapse_net.inference.util import inference_helper, parse_tiling def run_vesicle_segmentation(args): diff --git a/scripts/cooper/training/train_AZ.py b/scripts/cooper/training/train_AZ.py index 1468eaf..15cb1cd 100644 --- a/scripts/cooper/training/train_AZ.py +++ b/scripts/cooper/training/train_AZ.py @@ -8,11 +8,11 @@ from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training import supervised_training -from synaptic_reconstruction.training import semisupervised_training +from synapse_net.training import supervised_training +from synapse_net.training import semisupervised_training TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/exported_imod_objects" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/training_AZ_v1" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/training_AZ_v1" def _require_train_val_test_split(datasets): @@ -112,7 +112,7 @@ def train(key, ignore_label = None, training_2D = False, testset = True): sampler = torch_em.data.sampler.MinInstanceSampler(min_num_instances=1), n_samples_train=None, n_samples_val=25, check=check, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/AZ_models", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/AZ_models", n_iterations=int(5e3), ignore_label= ignore_label, label_transform=torch_em.transform.label.labels_to_binary, diff --git a/scripts/cooper/training/train_compartments.py b/scripts/cooper/training/train_compartments.py index a72cb28..5d568c5 100644 --- a/scripts/cooper/training/train_compartments.py +++ b/scripts/cooper/training/train_compartments.py @@ -11,7 +11,7 @@ from skimage.morphology import disk from scipy.ndimage import binary_dilation, distance_transform_edt -from synaptic_reconstruction.training import supervised_training +from synapse_net.training import supervised_training TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/ground_truth/compartments" # TRAIN_ROOT = "/home/pape/Work/my_projects/synaptic-reconstruction/scripts/cooper/ground_truth/compartments/output/compartment_gt" # noqa diff --git a/scripts/cooper/training/train_vesicles.py b/scripts/cooper/training/train_vesicles.py index 7f60943..bca7c7b 100644 --- a/scripts/cooper/training/train_vesicles.py +++ b/scripts/cooper/training/train_vesicles.py @@ -5,11 +5,11 @@ from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training import supervised_training -from synaptic_reconstruction.training import semisupervised_training +from synapse_net.training import supervised_training +from synapse_net.training import semisupervised_training TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/vesicles_processed_v2" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/training_v2" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/training_v2" def _require_train_val_test_split(datasets): @@ -111,7 +111,7 @@ def train(key, ignore_label = None, training_2D = False, testset = True): patch_shape=patch_shape, batch_size=batch_size, n_samples_train=None, n_samples_val=25, check=check, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/models_v2", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models_v2", ignore_label= ignore_label, ) diff --git a/scripts/cooper/vesicle_segmentation_h5.py b/scripts/cooper/vesicle_segmentation_h5.py index 9c8b1d1..0237973 100644 --- a/scripts/cooper/vesicle_segmentation_h5.py +++ b/scripts/cooper/vesicle_segmentation_h5.py @@ -6,8 +6,8 @@ from tqdm import tqdm from elf.io import open_file -from synaptic_reconstruction.inference.vesicles import segment_vesicles -from synaptic_reconstruction.inference.util import parse_tiling +from synapse_net.inference.vesicles import segment_vesicles +from synapse_net.inference.util import parse_tiling def _require_output_folders(output_folder): #seg_output = os.path.join(output_folder, "segmentations") diff --git a/scripts/cryo/actin/predict_actin.py b/scripts/cryo/actin/predict_actin.py index a247261..b6aa347 100644 --- a/scripts/cryo/actin/predict_actin.py +++ b/scripts/cryo/actin/predict_actin.py @@ -5,7 +5,7 @@ import h5py import numpy as np from elf.io import open_file -from synaptic_reconstruction.inference.actin import segment_actin +from synapse_net.inference.actin import segment_actin # Run prediction on the actin val volume. diff --git a/scripts/cryo/actin/train_actin_segmentation.py b/scripts/cryo/actin/train_actin_segmentation.py index 18b52e1..1b3c0cb 100644 --- a/scripts/cryo/actin/train_actin_segmentation.py +++ b/scripts/cryo/actin/train_actin_segmentation.py @@ -1,6 +1,6 @@ import numpy as np -from synaptic_reconstruction.training import supervised_training +from synapse_net.training import supervised_training from torch_em.data.sampler import MinForegroundSampler diff --git a/scripts/cryo/actin/train_domain_adaptation.py b/scripts/cryo/actin/train_domain_adaptation.py index 6d92112..456d55f 100644 --- a/scripts/cryo/actin/train_domain_adaptation.py +++ b/scripts/cryo/actin/train_domain_adaptation.py @@ -1,5 +1,5 @@ import os -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/fernandez-busnadiego/from_arsen/tomos_actin_18924" # noqa diff --git a/scripts/cryo/vesicles/debug_vesicle_seg.py b/scripts/cryo/vesicles/debug_vesicle_seg.py index 2d86fe7..588e24e 100644 --- a/scripts/cryo/vesicles/debug_vesicle_seg.py +++ b/scripts/cryo/vesicles/debug_vesicle_seg.py @@ -1,7 +1,7 @@ import h5py import napari -from synaptic_reconstruction.inference.vesicles import distance_based_vesicle_segmentation +from synapse_net.inference.vesicles import distance_based_vesicle_segmentation def debug_vesicle_seg(path, pred_path): diff --git a/scripts/cryo/vesicles/train_domain_adaptation.py b/scripts/cryo/vesicles/train_domain_adaptation.py index 9270ba4..cf990d8 100644 --- a/scripts/cryo/vesicles/train_domain_adaptation.py +++ b/scripts/cryo/vesicles/train_domain_adaptation.py @@ -4,10 +4,10 @@ import json from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/fernandez-busnadiego/from_arsen" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_training" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_training" def _require_train_val_test_split(datasets): train_ratio, val_ratio, test_ratio = 0.8, 0.1, 0.1 @@ -86,7 +86,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): patch_shape = [48, 256, 256] model_name = "vesicle-DA-cryo-v2" - model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/models_v2/checkpoints/" + model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models_v2/checkpoints/" checkpoint_path = os.path.join(model_root, teacher_model) mean_teacher_adaptation( @@ -95,7 +95,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): unsupervised_val_paths=val_paths, raw_key="data", patch_shape=patch_shape, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_models", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_models", source_checkpoint=checkpoint_path, confidence_threshold=0.75, n_iterations=int(5e4), diff --git a/scripts/inner_ear/analysis/analyze_vesicle_diameters.py b/scripts/inner_ear/analysis/analyze_vesicle_diameters.py index d41dbe6..69227be 100644 --- a/scripts/inner_ear/analysis/analyze_vesicle_diameters.py +++ b/scripts/inner_ear/analysis/analyze_vesicle_diameters.py @@ -7,8 +7,8 @@ import pandas as pd from tqdm import tqdm -from synaptic_reconstruction.imod.export import load_points_from_imodinfo -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.imod.export import load_points_from_imodinfo +from synapse_net.file_utils import get_data_path from common import get_finished_tomos diff --git a/scripts/inner_ear/analysis/check_outliers.py b/scripts/inner_ear/analysis/check_outliers.py index 353a042..d88e8e6 100644 --- a/scripts/inner_ear/analysis/check_outliers.py +++ b/scripts/inner_ear/analysis/check_outliers.py @@ -3,7 +3,7 @@ import imageio.v3 as imageio import napari -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from elf.io import open_file diff --git a/scripts/inner_ear/analysis/check_radii.py b/scripts/inner_ear/analysis/check_radii.py index 3fba1e2..593f11f 100644 --- a/scripts/inner_ear/analysis/check_radii.py +++ b/scripts/inner_ear/analysis/check_radii.py @@ -8,7 +8,7 @@ from elf.io import open_file from tqdm import tqdm -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path sys.path.append("../processing") @@ -79,7 +79,7 @@ def check_diameter_results(): def test_export(): - from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod_as_points + from synapse_net.imod.to_imod import write_segmentation_to_imod_as_points from subprocess import run mrc_path = "/home/pape/Work/data/moser/em-synapses/Electron-Microscopy-Susi/Analyse/WT strong stim/Mouse 1/pillar/1/Emb71M1aGridA3sec3pil12.rec" # noqa diff --git a/scripts/inner_ear/analysis/export_seg_to_imod.py b/scripts/inner_ear/analysis/export_seg_to_imod.py index eea4b14..04144c5 100644 --- a/scripts/inner_ear/analysis/export_seg_to_imod.py +++ b/scripts/inner_ear/analysis/export_seg_to_imod.py @@ -9,7 +9,7 @@ import pandas as pd from elf.io import open_file from skimage.transform import resize -from synaptic_reconstruction.imod.to_imod import write_segmentation_to_imod, write_segmentation_to_imod_as_points +from synapse_net.imod.to_imod import write_segmentation_to_imod, write_segmentation_to_imod_as_points out_folder = "./auto_seg_export" os.makedirs(out_folder, exist_ok=True) diff --git a/scripts/inner_ear/check_manual_analysis.py b/scripts/inner_ear/check_manual_analysis.py index c8ccd27..f4da93b 100644 --- a/scripts/inner_ear/check_manual_analysis.py +++ b/scripts/inner_ear/check_manual_analysis.py @@ -6,13 +6,13 @@ import napari import numpy as np -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from elf.io import open_file from tqdm import tqdm from napari_skimage_regionprops import add_table -from synaptic_reconstruction.tools.distance_measurement import _downsample +from synapse_net.tools.distance_measurement import _downsample from check_results import get_distance_visualization, create_vesicle_pools, _update_colors sys.path.append("processing") diff --git a/scripts/inner_ear/check_results.py b/scripts/inner_ear/check_results.py index 101481a..7bf3e5d 100644 --- a/scripts/inner_ear/check_results.py +++ b/scripts/inner_ear/check_results.py @@ -9,8 +9,8 @@ import numpy as np import pandas -from synaptic_reconstruction.distance_measurements import create_object_distance_lines, load_distances -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.distance_measurements import create_object_distance_lines, load_distances +from synapse_net.file_utils import get_data_path from elf.io import open_file from skimage.transform import rescale, resize diff --git a/scripts/inner_ear/ground_truth/extract_automatic_structures.py b/scripts/inner_ear/ground_truth/extract_automatic_structures.py index f416964..92ba226 100644 --- a/scripts/inner_ear/ground_truth/extract_automatic_structures.py +++ b/scripts/inner_ear/ground_truth/extract_automatic_structures.py @@ -8,8 +8,8 @@ import pandas from elf.io import open_file -from synaptic_reconstruction.file_utils import get_data_path -from synaptic_reconstruction.tools.distance_measurement import _downsample +from synapse_net.file_utils import get_data_path +from synapse_net.tools.distance_measurement import _downsample from tqdm import tqdm sys.path.append("../processing") diff --git a/scripts/inner_ear/processing/analyze_manual_annotations.py b/scripts/inner_ear/processing/analyze_manual_annotations.py index 81231b1..018bc7b 100644 --- a/scripts/inner_ear/processing/analyze_manual_annotations.py +++ b/scripts/inner_ear/processing/analyze_manual_annotations.py @@ -2,7 +2,7 @@ import mrcfile from elf.io import open_file -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from tqdm import tqdm from parse_table import parse_table, get_data_root diff --git a/scripts/inner_ear/processing/check_resolutions.py b/scripts/inner_ear/processing/check_resolutions.py index 7ccbb71..e01d2b8 100644 --- a/scripts/inner_ear/processing/check_resolutions.py +++ b/scripts/inner_ear/processing/check_resolutions.py @@ -4,7 +4,7 @@ import numpy as np from tqdm import tqdm -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from parse_table import parse_table, get_data_root diff --git a/scripts/inner_ear/processing/compute_morphology.py b/scripts/inner_ear/processing/compute_morphology.py index eefd07f..4b16dc9 100644 --- a/scripts/inner_ear/processing/compute_morphology.py +++ b/scripts/inner_ear/processing/compute_morphology.py @@ -6,8 +6,8 @@ from tqdm import tqdm from elf.io import open_file -from synaptic_reconstruction.morphology import compute_radii -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.morphology import compute_radii +from synapse_net.file_utils import get_data_path from run_analyis import _load_segmentation, compute_morphology, to_excel from parse_table import parse_table, get_data_root, _match_correction_folder, _match_correction_file diff --git a/scripts/inner_ear/processing/process_manual_segmentation.py b/scripts/inner_ear/processing/process_manual_segmentation.py index 72e19e3..b111eda 100644 --- a/scripts/inner_ear/processing/process_manual_segmentation.py +++ b/scripts/inner_ear/processing/process_manual_segmentation.py @@ -11,8 +11,8 @@ from skimage.transform import rescale from tqdm import tqdm -from synaptic_reconstruction.imod import export_segmentation, export_point_annotations -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.imod import export_segmentation, export_point_annotations +from synapse_net.file_utils import get_data_path from parse_table import parse_table, get_data_root diff --git a/scripts/inner_ear/processing/refine_vesicle_shapes.py b/scripts/inner_ear/processing/refine_vesicle_shapes.py index 8f26394..42640e8 100644 --- a/scripts/inner_ear/processing/refine_vesicle_shapes.py +++ b/scripts/inner_ear/processing/refine_vesicle_shapes.py @@ -5,8 +5,8 @@ import numpy as np from elf.io import open_file -from synaptic_reconstruction.ground_truth.shape_refinement import edge_filter, refine_vesicle_shapes -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.ground_truth.shape_refinement import edge_filter, refine_vesicle_shapes +from synapse_net.file_utils import get_data_path from parse_table import get_data_root, parse_table from tqdm import tqdm diff --git a/scripts/inner_ear/processing/rescale_tomogram.py b/scripts/inner_ear/processing/rescale_tomogram.py index 1d0a0c8..bec8b9f 100644 --- a/scripts/inner_ear/processing/rescale_tomogram.py +++ b/scripts/inner_ear/processing/rescale_tomogram.py @@ -5,7 +5,7 @@ import mrcfile from skimage.transform import rescale -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from parse_table import get_data_root diff --git a/scripts/inner_ear/processing/run_analyis.py b/scripts/inner_ear/processing/run_analyis.py index fbb00f1..ed6ccdd 100644 --- a/scripts/inner_ear/processing/run_analyis.py +++ b/scripts/inner_ear/processing/run_analyis.py @@ -8,15 +8,15 @@ import pandas import vigra -from synaptic_reconstruction.file_utils import get_data_path -from synaptic_reconstruction.distance_measurements import ( +from synapse_net.file_utils import get_data_path +from synapse_net.distance_measurements import ( filter_blocked_segmentation_to_object_distances, load_distances, measure_segmentation_to_object_distances, ) -from synaptic_reconstruction.morphology import compute_radii, compute_object_morphology -from synaptic_reconstruction.inference.postprocessing import filter_border_vesicles +from synapse_net.morphology import compute_radii, compute_object_morphology +from synapse_net.inference.postprocessing import filter_border_vesicles from skimage.transform import resize from skimage.measure import regionprops, label diff --git a/scripts/inner_ear/processing/run_structure_postprocessing.py b/scripts/inner_ear/processing/run_structure_postprocessing.py index 54be1a3..b0307f6 100644 --- a/scripts/inner_ear/processing/run_structure_postprocessing.py +++ b/scripts/inner_ear/processing/run_structure_postprocessing.py @@ -4,8 +4,8 @@ import mrcfile import imageio.v2 as imageio -import synaptic_reconstruction.inference.postprocessing as postprocessing -from synaptic_reconstruction.file_utils import get_data_path +import synapse_net.inference.postprocessing as postprocessing +from synapse_net.file_utils import get_data_path from elf.io import open_file from tqdm import tqdm diff --git a/scripts/inner_ear/processing/run_structure_prediction.py b/scripts/inner_ear/processing/run_structure_prediction.py index f1e4697..2052fdd 100644 --- a/scripts/inner_ear/processing/run_structure_prediction.py +++ b/scripts/inner_ear/processing/run_structure_prediction.py @@ -5,18 +5,18 @@ from tqdm import tqdm from elf.io import open_file -from synaptic_reconstruction.file_utils import get_data_path -from synaptic_reconstruction.inference import segment_structures +from synapse_net.file_utils import get_data_path +from synapse_net.inference import segment_structures from parse_table import parse_table, get_data_root VERSIONS = { 1: { - "model": "/scratch/projects/nim00007/data/synaptic_reconstruction/models/moser/structures/supervised-v4.zip", + "model": "/scratch/projects/nim00007/data/synapse_net/models/moser/structures/supervised-v4.zip", }, 2: { - "model": "/scratch/projects/nim00007/data/synaptic_reconstruction/models/moser/structures/supervised-v4.zip", + "model": "/scratch/projects/nim00007/data/synapse_net/models/moser/structures/supervised-v4.zip", # The new model doesn't actually work better. it predicts too much for PD and for Ribbon. - # "model": "/scratch/projects/nim00007/data/synaptic_reconstruction/models/moser/structures/supervised-v5.zip", + # "model": "/scratch/projects/nim00007/data/synapse_net/models/moser/structures/supervised-v5.zip", }, } diff --git a/scripts/inner_ear/processing/run_vesicle_segmentation.py b/scripts/inner_ear/processing/run_vesicle_segmentation.py index 83f70da..549f039 100644 --- a/scripts/inner_ear/processing/run_vesicle_segmentation.py +++ b/scripts/inner_ear/processing/run_vesicle_segmentation.py @@ -4,18 +4,18 @@ from tqdm import tqdm from elf.io import open_file -from synaptic_reconstruction.file_utils import get_data_path -from synaptic_reconstruction.inference import segment_vesicles -from synaptic_reconstruction.inference.postprocessing import close_holes +from synapse_net.file_utils import get_data_path +from synapse_net.inference import segment_vesicles +from synapse_net.inference.postprocessing import close_holes from parse_table import parse_table, get_data_root VERSIONS = { 1: { - "model": "/scratch/projects/nim00007/data/synaptic_reconstruction/models/moser/vesicles/mean-teacher-v3.zip", + "model": "/scratch/projects/nim00007/data/synapse_net/models/moser/vesicles/mean-teacher-v3.zip", "distance_based_segmentation": True, }, 2: { - "model": "/scratch/projects/nim00007/data/synaptic_reconstruction/models/moser/vesicles/mean-teacher-v5.zip", + "model": "/scratch/projects/nim00007/data/synapse_net/models/moser/vesicles/mean-teacher-v5.zip", "distance_based_segmentation": True, "closing_iterations": 4, } diff --git a/scripts/inner_ear/training/postprocessing_and_evaluation.py b/scripts/inner_ear/training/postprocessing_and_evaluation.py index 30c1313..af84904 100644 --- a/scripts/inner_ear/training/postprocessing_and_evaluation.py +++ b/scripts/inner_ear/training/postprocessing_and_evaluation.py @@ -5,15 +5,15 @@ import pandas as pd from elf.evaluation.dice import dice_score -from synaptic_reconstruction.inference.vesicles import segment_vesicles -from synaptic_reconstruction.inference.postprocessing.ribbon import segment_ribbon -from synaptic_reconstruction.inference.postprocessing.presynaptic_density import segment_presynaptic_density +from synapse_net.inference.vesicles import segment_vesicles +from synapse_net.inference.postprocessing.ribbon import segment_ribbon +from synapse_net.inference.postprocessing.presynaptic_density import segment_presynaptic_density from torch_em.util import load_model from tqdm import tqdm from train_structure_segmentation import get_train_val_test_split -# ROOT = "/home/pape/Work/data/synaptic_reconstruction/moser" +# ROOT = "/home/pape/Work/data/synapse_net/moser" ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/moser" MODEL_PATH = "/mnt/lustre-emmy-hdd/projects/nim00007/models/synaptic-reconstruction/vesicle-DA-inner_ear-v2" OUTPUT_ROOT = "./predictions" diff --git a/scripts/inner_ear/training/structure_prediction_and_evaluation.py b/scripts/inner_ear/training/structure_prediction_and_evaluation.py index 7ed89a9..7930cea 100644 --- a/scripts/inner_ear/training/structure_prediction_and_evaluation.py +++ b/scripts/inner_ear/training/structure_prediction_and_evaluation.py @@ -4,7 +4,7 @@ import h5py import pandas as pd from elf.evaluation.dice import dice_score -from synaptic_reconstruction.inference.ribbon_synapse import segment_ribbon_synapse_structures +from synapse_net.inference.ribbon_synapse import segment_ribbon_synapse_structures from torch_em.util import load_model from tqdm import tqdm @@ -12,7 +12,7 @@ from train_structure_segmentation import noop # noqa ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/moser" -# ROOT = "/home/pape/Work/data/synaptic_reconstruction/moser" +# ROOT = "/home/pape/Work/data/synapse_net/moser" OUTPUT_ROOT = "./predictions" diff --git a/scripts/inner_ear/training/train_domain_adaptation.py b/scripts/inner_ear/training/train_domain_adaptation.py index d5f5bc0..239ca9f 100644 --- a/scripts/inner_ear/training/train_domain_adaptation.py +++ b/scripts/inner_ear/training/train_domain_adaptation.py @@ -3,7 +3,7 @@ import numpy as np from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation from train_structure_segmentation import noop # noqa diff --git a/scripts/inner_ear/training/train_domain_adaptation_vesicles.py b/scripts/inner_ear/training/train_domain_adaptation_vesicles.py index e447172..8be86ac 100644 --- a/scripts/inner_ear/training/train_domain_adaptation_vesicles.py +++ b/scripts/inner_ear/training/train_domain_adaptation_vesicles.py @@ -4,10 +4,10 @@ import json from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/moser/inner_ear_data" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_training_inner_ear" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_training_inner_ear" # Define a dictionary for skipped files TESTSET = { @@ -121,7 +121,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): patch_shape = [48, 256, 256] model_name = "vesicle-DA-inner_ear-v2" - model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/models_v2/checkpoints/" + model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models_v2/checkpoints/" checkpoint_path = os.path.join(model_root, teacher_model) mean_teacher_adaptation( @@ -130,7 +130,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): unsupervised_val_paths=val_paths, raw_key="raw", patch_shape=patch_shape, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_models", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_models", source_checkpoint=checkpoint_path, confidence_threshold=0.75, n_iterations=int(1e5), diff --git a/scripts/inner_ear/training/train_structure_segmentation.py b/scripts/inner_ear/training/train_structure_segmentation.py index 96c4747..0f43422 100644 --- a/scripts/inner_ear/training/train_structure_segmentation.py +++ b/scripts/inner_ear/training/train_structure_segmentation.py @@ -4,7 +4,7 @@ import h5py import numpy as np -from synaptic_reconstruction.training.supervised_training import supervised_training +from synapse_net.training.supervised_training import supervised_training from sklearn.model_selection import train_test_split from torch_em.data.sampler import MinForegroundSampler from tqdm import tqdm diff --git a/scripts/inner_ear/validate_segmentations.py b/scripts/inner_ear/validate_segmentations.py index d47f5bc..ce5292a 100644 --- a/scripts/inner_ear/validate_segmentations.py +++ b/scripts/inner_ear/validate_segmentations.py @@ -4,7 +4,7 @@ import pandas -from synaptic_reconstruction.file_utils import get_data_path +from synapse_net.file_utils import get_data_path from elf.io import open_file from tqdm import tqdm diff --git a/scripts/inner_ear/vesicle_annotation.py b/scripts/inner_ear/vesicle_annotation.py index 6c917d1..53f132d 100644 --- a/scripts/inner_ear/vesicle_annotation.py +++ b/scripts/inner_ear/vesicle_annotation.py @@ -32,7 +32,7 @@ def _size_filter(segmentation, min_size): def create_data_for_vesicle_annotation(view=True): - from synaptic_reconstruction.ground_truth import find_additional_objects + from synapse_net.ground_truth import find_additional_objects table = pd.read_excel(os.path.join(ROOT, "Validierungs-Tabelle-v3.xlsx")) diff --git a/scripts/liposomes/measure_distances.py b/scripts/liposomes/measure_distances.py index bb0c66a..21935c8 100644 --- a/scripts/liposomes/measure_distances.py +++ b/scripts/liposomes/measure_distances.py @@ -7,8 +7,8 @@ import pandas as pd from elf.io import open_file -from synaptic_reconstruction.distance_measurements import measure_pairwise_object_distances -from synaptic_reconstruction.tools.distance_measurement import measure_distances, _downsample, create_distance_lines +from synapse_net.distance_measurements import measure_pairwise_object_distances +from synapse_net.tools.distance_measurement import measure_distances, _downsample, create_distance_lines # ON WORKSTATION TOMO_ROOT = "/home/user2/data/corrected_tomos_mrc" diff --git a/scripts/rizzoli/2D_vesicle_segmentation.py b/scripts/rizzoli/2D_vesicle_segmentation.py index 7974e3b..5c20e15 100644 --- a/scripts/rizzoli/2D_vesicle_segmentation.py +++ b/scripts/rizzoli/2D_vesicle_segmentation.py @@ -8,8 +8,8 @@ import torch_em import numpy as np -from synaptic_reconstruction.inference.vesicles import segment_vesicles -from synaptic_reconstruction.inference.util import parse_tiling +from synapse_net.inference.vesicles import segment_vesicles +from synapse_net.inference.util import parse_tiling def get_2D_tiling(): """Determine the tile shape and halo depending on the available VRAM. diff --git a/scripts/frog_synapses/data_extraction/.gitignore b/scripts/rizzoli/data_extraction/.gitignore similarity index 100% rename from scripts/frog_synapses/data_extraction/.gitignore rename to scripts/rizzoli/data_extraction/.gitignore diff --git a/scripts/frog_synapses/data_extraction/automatic_labeling.py b/scripts/rizzoli/data_extraction/automatic_labeling.py similarity index 100% rename from scripts/frog_synapses/data_extraction/automatic_labeling.py rename to scripts/rizzoli/data_extraction/automatic_labeling.py diff --git a/scripts/frog_synapses/data_extraction/common.py b/scripts/rizzoli/data_extraction/common.py similarity index 100% rename from scripts/frog_synapses/data_extraction/common.py rename to scripts/rizzoli/data_extraction/common.py diff --git a/scripts/frog_synapses/data_extraction/extract_data.py b/scripts/rizzoli/data_extraction/extract_data.py similarity index 100% rename from scripts/frog_synapses/data_extraction/extract_data.py rename to scripts/rizzoli/data_extraction/extract_data.py diff --git a/scripts/frog_synapses/data_extraction/initial_slice_annotation.py b/scripts/rizzoli/data_extraction/initial_slice_annotation.py similarity index 100% rename from scripts/frog_synapses/data_extraction/initial_slice_annotation.py rename to scripts/rizzoli/data_extraction/initial_slice_annotation.py diff --git a/scripts/frog_synapses/data_extraction/train_sam_model.py b/scripts/rizzoli/data_extraction/train_sam_model.py similarity index 100% rename from scripts/frog_synapses/data_extraction/train_sam_model.py rename to scripts/rizzoli/data_extraction/train_sam_model.py diff --git a/scripts/rizzoli/train_2D_domain_adaptation.py b/scripts/rizzoli/train_2D_domain_adaptation.py index 86eedd1..3acfb33 100644 --- a/scripts/rizzoli/train_2D_domain_adaptation.py +++ b/scripts/rizzoli/train_2D_domain_adaptation.py @@ -4,10 +4,10 @@ import json from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/rizzoli/extracted" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/2D_DA_training_rizzoli" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/2D_DA_training_rizzoli" def _require_train_val_test_split(datasets): train_ratio, val_ratio, test_ratio = 0.8, 0.1, 0.1 @@ -85,7 +85,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): patch_shape = [1, 256, 256] #2D model_name = "2D-vesicle-DA-rizzoli-v3" - model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/models_v2/checkpoints/" + model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models_v2/checkpoints/" checkpoint_path = os.path.join(model_root, teacher_model) mean_teacher_adaptation( @@ -94,7 +94,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): unsupervised_val_paths=val_paths, raw_key="raw", patch_shape=patch_shape, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_models", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_models", source_checkpoint=checkpoint_path, confidence_threshold=0.75, n_iterations=int(5e4), diff --git a/scripts/wichmann/export_vesicles_from_imod.py b/scripts/wichmann/export_vesicles_from_imod.py index 27736ab..566b7a9 100644 --- a/scripts/wichmann/export_vesicles_from_imod.py +++ b/scripts/wichmann/export_vesicles_from_imod.py @@ -4,7 +4,7 @@ import argparse import sys sys.path.append('/home/smuth/Documents/PhD/code/synaptic-reconstruction') -from synaptic_reconstruction.ground_truth import extract_vesicle_training_data +from synapse_net.ground_truth import extract_vesicle_training_data ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/wichmann/original_imod_data/endbulb_of_held/Adult" # noqa OUT_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/wichmann/extracted/endbulb_of_held/Adult" # noqa diff --git a/scripts/wichmann/train_domain_adaptation.py b/scripts/wichmann/train_domain_adaptation.py index 9727d4c..3d5da3c 100644 --- a/scripts/wichmann/train_domain_adaptation.py +++ b/scripts/wichmann/train_domain_adaptation.py @@ -4,10 +4,10 @@ import json from sklearn.model_selection import train_test_split -from synaptic_reconstruction.training.domain_adaptation import mean_teacher_adaptation +from synapse_net.training.domain_adaptation import mean_teacher_adaptation TRAIN_ROOT = "/mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/wichmann/extracted/endbulb_of_held/" -OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_training_endbulb_v2" +OUTPUT_ROOT = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_training_endbulb_v2" def _require_train_val_test_split(datasets): train_ratio, val_ratio, test_ratio = 0.8, 0.1, 0.1 @@ -123,7 +123,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): patch_shape = [48, 256, 256] model_name = "vesicle-DA-endbulb-v3" - model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/models_v2/checkpoints/" + model_root = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models_v2/checkpoints/" checkpoint_path = os.path.join(model_root, teacher_model) mean_teacher_adaptation( @@ -132,7 +132,7 @@ def vesicle_domain_adaptation(teacher_model, testset = True): unsupervised_val_paths=val_paths, raw_key="raw", patch_shape=patch_shape, - save_root="/mnt/lustre-emmy-hdd/usr/u12095/synaptic_reconstruction/DA_models", + save_root="/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/DA_models", source_checkpoint=checkpoint_path, confidence_threshold=0.75, n_iterations=int(5e4), diff --git a/test/test_cli.py b/test/test_cli.py index 6b0d1fb..b9e87e9 100644 --- a/test/test_cli.py +++ b/test/test_cli.py @@ -6,7 +6,7 @@ import imageio.v3 as imageio import mrcfile import pooch -from synaptic_reconstruction.sample_data import get_sample_data +from synapse_net.sample_data import get_sample_data class TestCLI(unittest.TestCase): diff --git a/test/test_distance_measurement.py b/test/test_distance_measurement.py index f3ed296..bf2a69b 100644 --- a/test/test_distance_measurement.py +++ b/test/test_distance_measurement.py @@ -5,7 +5,7 @@ class TestDistanceMeasurement(unittest.TestCase): def test_measure_pairwise_object_distances(self): - from synaptic_reconstruction.distance_measurements import measure_pairwise_object_distances + from synapse_net.distance_measurements import measure_pairwise_object_distances shape = (4, 64, 64) seg = np.zeros(shape, dtype="uint32") diff --git a/test/test_file_utils.py b/test/test_file_utils.py index 362f87f..68f234b 100644 --- a/test/test_file_utils.py +++ b/test/test_file_utils.py @@ -2,13 +2,13 @@ import numpy as np from elf.io import open_file -from synaptic_reconstruction.sample_data import get_sample_data +from synapse_net.sample_data import get_sample_data class TestFileUtils(unittest.TestCase): def test_read_mrc_2d(self): - from synaptic_reconstruction.file_utils import read_mrc + from synapse_net.file_utils import read_mrc file_path = get_sample_data("tem_2d") data, voxel_size = read_mrc(file_path) @@ -25,7 +25,7 @@ def test_read_mrc_2d(self): self.assertTrue(np.isclose(voxel_size["z"], 0.0)) def test_read_mrc_3d(self): - from synaptic_reconstruction.file_utils import read_mrc + from synapse_net.file_utils import read_mrc file_path = get_sample_data("tem_tomo") data, voxel_size = read_mrc(file_path)