DeepLabCut · MMathisLab · Dec 22, 2022 · Dec 14, 2022 · Dec 14, 2022 · Dec 14, 2022
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -2,9 +2,9 @@ name: Python package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:
@@ -30,10 +30,10 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/NOTICE.yml b/NOTICE.yml
@@ -1,11 +1,11 @@
 # 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 
+# When adding code from an external repo, make sure to cover the
 # added code files with the correct license header.
 
 # Main repository license
@@ -20,7 +20,7 @@
     Licensed under GNU Lesser General Public License v3.0
   include:
     - 'deeplabcut/**/*.py'
-    - 'tests/**/*.py' 
+    - 'tests/**/*.py'
     - 'examples/**/*.py'
     - 'docs/**/*.py'
     - 'conda-environments/**/*.yaml'
@@ -61,13 +61,13 @@
 # Tensorflow licenses
 - header: |
     Copyright 2019 The TensorFlow Authors. All Rights Reserved.
-    
+
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
-    
+
         http://www.apache.org/licenses/LICENSE-2.0
-    
+
     Unless required by applicable law or agreed to in writing, software
     distributed under the License is distributed on an "AS IS" BASIS,
     WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -85,7 +85,7 @@
     You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
-    
+
     Unless required by applicable law or agreed to in writing, software
     distributed under the License is distributed on an "AS IS" BASIS,
     WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -116,3 +116,23 @@
     https://github.com/rwightman/pytorch-image-models/blob/main/timm/scheduler/scheduler_factory.py
   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/deeplabcut/__init__.py b/deeplabcut/__init__.py
@@ -1,12 +1,14 @@
-"""
-DeepLabCut2.0 Toolbox (deeplabcut.org)
-© A. & M. Mathis Labs
-https://github.com/DeepLabCut/DeepLabCut
+#
+# 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
+#
 
-Please see AUTHORS for contributors.
-https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
-Licensed under GNU Lesser General Public License v3.0
-"""
 
 import os
 
@@ -121,4 +123,3 @@
     find_outliers_in_raw_data,
 )
 from deeplabcut.post_processing import filterpredictions, analyzeskeleton
-
diff --git a/deeplabcut/__main__.py b/deeplabcut/__main__.py
@@ -1,12 +1,14 @@
-"""
-DeepLabCut2.0 Toolbox (deeplabcut.org)
-© A. & M. Mathis Labs
-https://github.com/DeepLabCut/DeepLabCut
+#
+# 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
+#
 
-Please see AUTHORS for contributors.
-https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
-Licensed under GNU Lesser General Public License v3.0
-"""
 try:
     import PySide6
 

diff --git a/deeplabcut/benchmark/__init__.py b/deeplabcut/benchmark/__init__.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 
 import json

diff --git a/deeplabcut/benchmark/__main__.py b/deeplabcut/benchmark/__main__.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 from deeplabcut.benchmark.cli import main
 

diff --git a/deeplabcut/benchmark/base.py b/deeplabcut/benchmark/base.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 """Base classes for benchmark and result definition
 

diff --git a/deeplabcut/benchmark/benchmarks.py b/deeplabcut/benchmark/benchmarks.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 """Definition for official DeepLabCut benchmark tasks.
 

diff --git a/deeplabcut/benchmark/cli.py b/deeplabcut/benchmark/cli.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 """Command line interface for DeepLabCut deeplabcut.benchmark."""
 

diff --git a/deeplabcut/benchmark/metrics.py b/deeplabcut/benchmark/metrics.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 """Evaluation metrics for the DeepLabCut benchmark."""
 

diff --git a/deeplabcut/benchmark/utils.py b/deeplabcut/benchmark/utils.py
@@ -1,10 +1,13 @@
-# DeepLabCut2.0 Toolbox (deeplabcut.org)
-# © A. & M. Mathis Labs
-# https://github.com/AlexEMG/DeepLabCut
+#
+# 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
 #
-# https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
 # Licensed under GNU Lesser General Public License v3.0
+#
 
 """Helper functions in this file are not affected by the main repositories
 license. They are independent from the remainder of the benchmarking code. 

diff --git a/deeplabcut/cli.py b/deeplabcut/cli.py
@@ -1,12 +1,14 @@
-"""
-DeepLabCut2.0 Toolbox (deeplabcut.org)
-© A. & M. 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
-"""
+#
+# 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
 
 import click

diff --git a/deeplabcut/create_project/__init__.py b/deeplabcut/create_project/__init__.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 deeplabcut.create_project.add import add_new_videos
 from deeplabcut.create_project.demo_data import load_demo_data
 from deeplabcut.create_project.modelzoo import (

diff --git a/deeplabcut/create_project/add.py b/deeplabcut/create_project/add.py
@@ -1,12 +1,13 @@
-"""
-DeepLabCut2.2 Toolbox (deeplabcut.org)
-© A. & M. 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
-"""
+#
+# 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
+#
 
 
 def add_new_videos(config, videos, copy_videos=False, coords=None, extract_frames=False):
@@ -74,7 +75,7 @@ def add_new_videos(config, videos, copy_videos=False, coords=None, extract_frame
             else:
                 print("Copying the videos")
                 shutil.copy(os.fspath(src), os.fspath(dst))
-  
+
     else:
         # creates the symlinks of the video and puts it in the videos directory.
         print("Attempting to create a symbolic link of the video ...")
@@ -100,7 +101,7 @@ def add_new_videos(config, videos, copy_videos=False, coords=None, extract_frame
                     print("{} moved to {}".format(src, dst))
             videos = destinations
 
-    
+
 
     if copy_videos:
         videos = destinations  # in this case the *new* location should be added to the config file

diff --git a/deeplabcut/create_project/demo_data.py b/deeplabcut/create_project/demo_data.py
@@ -1,12 +1,13 @@
-"""
-DeepLabCut2.2 Toolbox (deeplabcut.org)
-© A. & M. 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
-"""
+#
+# 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
 from pathlib import Path
@@ -17,17 +18,17 @@
 
 def load_demo_data(config, createtrainingset=True):
     """
-    Loads the demo data -- subset from trail-tracking data in Mathis et al. 2018. 
+    Loads the demo data -- subset from trail-tracking data in Mathis et al. 2018.
     When loading, it sets paths correctly to run this project on your system
-    
+
     Parameter
       ----------
       config : string
           Full path of the config.yaml file of the provided demo dataset as a string.
 
-      createtrainingset : bool 
-          Boolean variable indicating if a training set shall be created. 
-          
+      createtrainingset : bool
+          Boolean variable indicating if a training set shall be created.
+
       Example
       --------
       >>> deeplabcut.load_demo_data('config.yaml')