V232 (DeepLabCut#2176)

* version update * update headers * header update * update notice file * black .
wer-kle · Mar 18, 2023 · 204310b · 204310b
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diff --git a/NOTICE.yml b/NOTICE.yml
@@ -1,13 +1,3 @@
-# This notice file contains license headers for all code files
-# in the repository (currently all *.py files).
-#
-# When updating headers, lower entries take precedence over higher
-# entries. For each header, include/exclude statements can be used
-# to define files to apply them to.
-#
-# When adding code from an external repo, make sure to cover the
-# added code files with the correct license header.
-
 # Main repository license
 - header: |
     DeepLabCut Toolbox (deeplabcut.org)
@@ -23,7 +13,7 @@
     - 'tests/**/*.py'
     - 'examples/**/*.py'
     - 'docs/**/*.py'
-    - 'conda-environments/**/*.yaml'
+    #- 'conda-environments/**/*.yaml'
 
 # License for files adapted from DeeperCut by Eldar Insafutdinov
 # https://github.com/eldar/pose-tensorflow
@@ -117,22 +107,3 @@
   include:
     - deeplabcut/pose_tracking_pytorch/solver/scheduler_factory.py
     - deeplabcut/pose_tracking_pytorch/model/backones/vit_pytorch.py
-
-# Reranking
-- header: |
-    """
-    CVPR2017 paper:Zhong Z, Zheng L, Cao D, et al. Re-ranking Person Re-identification with k-reciprocal Encoding[J]. 2017.
-    url:http://openaccess.thecvf.com/content_cvpr_2017/papers/Zhong_Re-Ranking_Person_Re-Identification_CVPR_2017_paper.pdf
-    Matlab version: https://github.com/zhunzhong07/person-re-ranking
-
-    API
-
-    probFea: all feature vectors of the query set (torch tensor)
-    probFea: all feature vectors of the gallery set (torch tensor)
-    k1,k2,lambda: parameters, the original paper is (k1=20,k2=6,lambda=0.3)
-    MemorySave: set to 'True' when using MemorySave mode
-    Minibatch: available when 'MemorySave' is 'True'
-    """
-
-  include:
-    - deeplabcut/pose_tracking_pytorch/trackingutils/reranking.py
diff --git a/conda-environments/DEEPLABCUT.yaml b/conda-environments/DEEPLABCUT.yaml
@@ -1,7 +1,7 @@
 # DEEPLABCUT.yaml
 
 #DeepLabCut2.0 Toolbox (deeplabcut.org)
-#© A. & M. Mathis Labs
+#© A. & M.W. Mathis Labs
 #https://github.com/DeepLabCut/DeepLabCut
 #Please see AUTHORS for contributors.
 

diff --git a/conda-environments/DEEPLABCUT_M1.yaml b/conda-environments/DEEPLABCUT_M1.yaml
@@ -1,7 +1,7 @@
 # DEEPLABCUT_M1.yaml
 
 #DeepLabCut2.0 Toolbox (deeplabcut.org)
-#© A. & M. Mathis Labs
+#© A. & M.W. Mathis Labs
 #https://github.com/DeepLabCut/DeepLabCut
 #Please see AUTHORS for contributors.
 

diff --git a/deeplabcut/gui/tabs/modelzoo.py b/deeplabcut/gui/tabs/modelzoo.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import deeplabcut
 from PySide6 import QtWidgets
 from PySide6.QtCore import Qt, Signal, QTimer

diff --git a/deeplabcut/modelzoo/__init__.py b/deeplabcut/modelzoo/__init__.py
@@ -0,0 +1,10 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
diff --git a/deeplabcut/modelzoo/api/__init__.py b/deeplabcut/modelzoo/api/__init__.py
@@ -1 +1,11 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 from .spatiotemporal_adapt import SpatiotemporalAdaptation
diff --git a/deeplabcut/modelzoo/api/spatiotemporal_adapt.py b/deeplabcut/modelzoo/api/spatiotemporal_adapt.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import deeplabcut
 import glob
 import os

diff --git a/deeplabcut/modelzoo/api/superanimal_inference.py b/deeplabcut/modelzoo/api/superanimal_inference.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import os
 import os.path
 import pickle

diff --git a/deeplabcut/modelzoo/utils.py b/deeplabcut/modelzoo/utils.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import json
 import os
 

diff --git a/deeplabcut/pose_estimation_tensorflow/predict_supermodel.py b/deeplabcut/pose_estimation_tensorflow/predict_supermodel.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 from pathlib import Path
 from deeplabcut.modelzoo.api import SpatiotemporalAdaptation
 

diff --git a/deeplabcut/pose_tracking_pytorch/model/backbones/vit_pytorch.py b/deeplabcut/pose_tracking_pytorch/model/backbones/vit_pytorch.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 """ Vision Transformer (ViT) in PyTorch
 
 A PyTorch implement of Vision Transformers as described in

diff --git a/deeplabcut/pose_tracking_pytorch/tracking_utils/reranking.py b/deeplabcut/pose_tracking_pytorch/tracking_utils/reranking.py
@@ -1,24 +1,31 @@
-"""
-CVPR2017 paper:Zhong Z, Zheng L, Cao D, et al. Re-ranking Person Re-identification with k-reciprocal Encoding[J]. 2017.
-url:http://openaccess.thecvf.com/content_cvpr_2017/papers/Zhong_Re-Ranking_Person_Re-Identification_CVPR_2017_paper.pdf
-Matlab version: https://github.com/zhunzhong07/person-re-ranking
-
-API
-
-probFea: all feature vectors of the query set (torch tensor)
-probFea: all feature vectors of the gallery set (torch tensor)
-k1,k2,lambda: parameters, the original paper is (k1=20,k2=6,lambda=0.3)
-MemorySave: set to 'True' when using MemorySave mode
-Minibatch: available when 'MemorySave' is 'True'
-"""
-
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import numpy as np
 import torch
 
 
 def re_ranking(
     probFea, galFea, k1, k2, lambda_value, local_distmat=None, only_local=False
 ):
+    """
+
+    probFea: all feature vectors of the query set (torch tensor)
+    galFea: all feature vectors of the gallery set (torch tensor)
+    k1,k2,lambda: parameters, the original paper uses (k1=20,k2=6,lambda=0.3)
+
+    Code adapted from  https://github.com/zhunzhong07/person-re-ranking
+
+    Zhong Z, Zheng L, Cao D, et al. Re-ranking Person Re-identification with k-reciprocal Encoding CVPR 2017.
+
+    """
     # if feature vector is numpy, you should use 'torch.tensor' transform it to tensor
     query_num = probFea.size(0)
     all_num = query_num + galFea.size(0)

diff --git a/deeplabcut/version.py b/deeplabcut/version.py
@@ -9,5 +9,5 @@
 # Licensed under GNU Lesser General Public License v3.0
 #
 
-__version__ = "2.3.1"
+__version__ = "2.3.2"
 VERSION = __version__
diff --git a/examples/test.sh b/examples/test.sh
@@ -6,7 +6,7 @@ rm -r OUT
 cd ..
 pip uninstall deeplabcut
 python3 setup.py sdist bdist_wheel
-pip install dist/deeplabcut-2.3.1-py3-none-any.whl
+pip install dist/deeplabcut-2.3.2-py3-none-any.whl
 
 cd examples
 

diff --git a/examples/testscript_superanimal_adaptation.py b/examples/testscript_superanimal_adaptation.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 """
 Test script for super animal adaptation
 """

diff --git a/examples/testscript_superanimal_inference.py b/examples/testscript_superanimal_inference.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 """
 Testscript for super animal inference
 

diff --git a/reinstall.sh b/reinstall.sh
@@ -1,3 +1,3 @@
 pip uninstall deeplabcut
 python3 setup.py sdist bdist_wheel
-pip install dist/deeplabcut-2.3.1-py3-none-any.whl
+pip install dist/deeplabcut-2.3.2-py3-none-any.whl
diff --git a/tests/test_predict_supermodel.py b/tests/test_predict_supermodel.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import numpy as np
 import pytest
 from deeplabcut.modelzoo.api import superanimal_inference

diff --git a/tests/tests_modelzoo.py b/tests/tests_modelzoo.py
@@ -1,3 +1,13 @@
+#
+# DeepLabCut Toolbox (deeplabcut.org)
+# © A. & M.W. Mathis Labs
+# https://github.com/DeepLabCut/DeepLabCut
+#
+# Please see AUTHORS for contributors.
+# https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+#
+# Licensed under GNU Lesser General Public License v3.0
+#
 import dlclibrary
 import os
 import pytest