Merge pull request #76 from computational-cell-analytics/clean-up

Clean up

Author: constantinpape

.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/

.gitignore

@@ -10,4 +10,5 @@ slurm/
 scripts/cooper/evaluation_results/
 scripts/cooper/training/copy_testset.py
 scripts/rizzoli/upsample_data.py
-scripts/cooper/training/find_rec_testset.py
+scripts/cooper/training/find_rec_testset.py
+synapse-net-models/

build_doc.py

@@ -11,6 +11,6 @@
 
     if args.out:
         cmd.extend(["--out", "tmp/"])
-    cmd.append("synaptic_reconstruction")
+    cmd.append("synapse_net")
 
     run(cmd)

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():

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():

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=64.0", "wheel"]
+build-backend = "setuptools.build_meta"

scripts/README.md

@@ -0,0 +1,5 @@
+# SynapseNet Scripts
+
+This folder contains scripts for several different projects that were either part of the SynapseNet publication, or that are part of a collaboration with other research groups.
+
+We will add an overview of the different scripts soon.

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

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

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