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[Auto-generated] Submodule Updates 33015311661 #93

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2 changes: 1 addition & 1 deletion repos/ac_reconstruction_analysis
Open in desktop
Submodule ac_reconstruction_analysis updated 82 files
+21 −0 .github/workflows/pixi.yml
+3 −3 .github/workflows/submodule-update.yml
+114 −0 .gitignore
+20 −0 Dockerfile
+674 −0 LICENSE
+0 −0 MANIFEST.in
+49 −1 README.md
+0 −18 acanalysis.egg-info/PKG-INFO
+0 −26 acanalysis.egg-info/SOURCES.txt
+0 −1 acanalysis.egg-info/dependency_links.txt
+0 −10 acanalysis.egg-info/requires.txt
+0 −2 acanalysis.egg-info/top_level.txt
+0 −0 acanalysis/__init__.py
+ − acanalysis/__pycache__/__init__.cpython-39.pyc
+ − acanalysis/__pycache__/save_cutout_for_segmentation.cpython-39.pyc
+ − acanalysis/__pycache__/splitup_swc.cpython-39.pyc
+ − acanalysis/__pycache__/utils.cpython-39.pyc
+ − acanalysis/__pycache__/write_swc_state.cpython-39.pyc
+0 −0 acanalysis/acalignment/__init__.py
+ − acanalysis/acalignment/__pycache__/__init__.cpython-39.pyc
+ − acanalysis/acalignment/__pycache__/generate_keypoints.cpython-39.pyc
+ − acanalysis/acalignment/__pycache__/keypoints.cpython-39.pyc
+ − acanalysis/acalignment/__pycache__/match_keypoints.cpython-39.pyc
+ − acanalysis/acalignment/__pycache__/transforms.cpython-39.pyc
+ − acanalysis/acalignment/__pycache__/utils.cpython-39.pyc
+0 −0 acanalysis/acalignment/examples/2_example_generate_keypoints.ipynb
+0 −0 acanalysis/acalignment/examples/3_example_match_keypoints.ipynb
+0 −0 acanalysis/acalignment/examples/align_S32_S33_roi1_mip0.json
+74 −20 acanalysis/acalignment/generate_keypoints.py
+0 −0 acanalysis/acalignment/keypoints.py
+0 −0 acanalysis/acalignment/match_keypoints.py
+0 −0 acanalysis/acalignment/transforms.py
+0 −0 acanalysis/acalignment/utils/__init__.py
+ − acanalysis/acalignment/utils/__pycache__/__init__.cpython-39.pyc
+ − acanalysis/acalignment/utils/__pycache__/kevin_utils.cpython-39.pyc
+ − acanalysis/acalignment/utils/__pycache__/olga_utils.cpython-39.pyc
+ − acanalysis/acalignment/utils/__pycache__/swc_utils.cpython-39.pyc
+557 −0 acanalysis/acalignment/utils/h5_utils.py
+160 −2 acanalysis/acalignment/utils/kevin_utils.py
+0 −0 acanalysis/acalignment/utils/olga_utils.py
+33 −4 acanalysis/acalignment/utils/swc_utils.py
+0 −0 acanalysis/odf/__init__.py
+38 −0 acanalysis/odf/plotting.py
+35 −0 acanalysis/odf/utils.py
+0 −0 acanalysis/save_cutout_for_segmentation.py
+0 −0 acanalysis/skeleton_reconstruction/__init__.py
+45 −0 acanalysis/skeleton_reconstruction/catmaid.py
+71 −0 acanalysis/skeleton_reconstruction/generate_precomputed_skels.py
+328 −0 acanalysis/skeleton_reconstruction/neuroglancer.py
+0 −0 acanalysis/skeleton_reconstruction/reconnection/__init__.py
+190 −0 acanalysis/skeleton_reconstruction/reconnection/create_components.py
+169 −0 acanalysis/skeleton_reconstruction/reconnection/find_pairs.py
+773 −0 acanalysis/skeleton_reconstruction/reconnection/h5_reconnect.py
+581 −0 acanalysis/skeleton_reconstruction/reconnection/h5_skeletons.py
+165 −0 acanalysis/skeleton_reconstruction/reconnection/merge_overlap.py
+151 −0 acanalysis/skeleton_reconstruction/reconnection/merge_pairs.py
+77 −0 acanalysis/skeleton_reconstruction/reconnection/reconnect_navis.py
+852 −0 acanalysis/skeleton_reconstruction/reconnection/utils.py
+0 −0 acanalysis/splitup_swc.py
+0 −0 acanalysis/utils.py
+0 −0 acanalysis/write_swc_state.py
+116 −0 demos/CATMAID_Functions.ipynb
+195 −0 demos/Neuroglancer_Functions.ipynb
+0 −0 demos/alignment/1_example_surface_detection.ipynb
+0 −0 demos/alignment/2_example_generate_keypoints.ipynb
+0 −0 demos/alignment/3_example_match_keypoints_new.ipynb
+0 −0 demos/alignment/4_example_skeleton_warp_updated.ipynb
+0 −0 demos/alignment/6_example_materialize_to_tiff.ipynb
+0 −0 demos/alignment/align_S32_S33_roi4_mip1_240408.json
+3 −0 entrypoint.sh
+ − examples/analysis/data/box_000.pkl
+ − examples/analysis/data/box_pos_5x10.pkl
+ − examples/analysis/data/mean_vectors_5x10.pkl
+ − examples/analysis/figures/skels_ori.pdf
+489 −0 examples/analysis/odf_analysis.ipynb
+71 −0 pyproject.toml
+7 −2 requirements.txt
+0 −21 setup.py
+0 −0 test/__init__.py
+ − test/model/LR_1.joblib
+ − test/model/scaler.joblib
+5 −1 test/test_import.py
2 changes: 1 addition & 1 deletion repos/ac_segmentation
Open in desktop
Submodule ac_segmentation updated 2 files
+2 −2 .github/workflows/ci.yml
+1 −1 .github/workflows/submodule-update.yml
2 changes: 1 addition & 1 deletion repos/axonal_connectomics
Open in desktop
Submodule axonal_connectomics updated 38 files
+4 −4 .github/workflows/ci.yml
+23 −0 .github/workflows/pixi.yml
+2 −2 .github/workflows/submodule-update.yml
+8 −0 .gitignore
+38 −16 README.md
+5 −2 acpreprocessing/deskewing.py
+107 −0 acpreprocessing/masking.py
+0 −0 acpreprocessing/stitching_modules/acstitch/__init__.py
+25 −0 acpreprocessing/stitching_modules/acstitch/ccorr_stitch.py
+132 −0 acpreprocessing/stitching_modules/acstitch/extract_points.py
+32 −0 acpreprocessing/stitching_modules/acstitch/io.py
+80 −0 acpreprocessing/stitching_modules/acstitch/rtccorr.py
+320 −0 acpreprocessing/stitching_modules/acstitch/sift_stitch.py
+86 −0 acpreprocessing/stitching_modules/acstitch/stitch.py
+63 −0 acpreprocessing/stitching_modules/acstitch/utils.py
+57 −0 acpreprocessing/stitching_modules/acstitch/zarrutils.py
+0 −141 acpreprocessing/stitching_modules/convert_to_n5/acquisition_dir_to_n5_dir.py
+191 −0 acpreprocessing/stitching_modules/convert_to_n5/acquisition_dir_to_ngff.py
+515 −0 acpreprocessing/stitching_modules/convert_to_n5/ims_to_ngff.py
+207 −0 acpreprocessing/stitching_modules/convert_to_n5/psdeskew.py
+377 −125 acpreprocessing/stitching_modules/convert_to_n5/tiff_to_ngff.py
+247 −0 acpreprocessing/stitching_modules/convert_to_n5/ts_utils.py
+465 −0 acpreprocessing/stitching_modules/convert_to_n5/zarr_to_ngff.py
+564 −0 acpreprocessing/stitching_modules/convert_to_n5/zarrv3_to_ngff.py
+0 −0 acpreprocessing/surface_detection/__init__.py
+109 −0 acpreprocessing/surface_detection/surface_detection.py
+174 −36 acpreprocessing/utils/ac_imageio.py
+5 −1 acpreprocessing/utils/convert.py
+34 −0 acpreprocessing/utils/logging.py
+7 −4 acpreprocessing/utils/nglink/update_state.py
+83 −0 pyproject.toml
+6 −2 requirements.txt
+0 −21 setup.cfg
+0 −25 setup.py
+3 −1 test/test_downsample.py
+17 −5 test/test_images.py
+13 −6 test/voltest.py
+0 −4 test_requirements.txt