autogaita 1.3.1__tar.gz → 1.4.0__tar.gz

{autogaita-1.3.1 → autogaita-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.3.1
+Version: 1.4.0
 Summary: Automatic Gait Analysis in Python. A toolbox to streamline and standardise the analysis of kinematics across species after ML-based body posture tracking. Despite being optimised for gait analyses, AutoGaitA has the potential to be used for any kind of kinematic analysis.
 Home-page: https://github.com/mahan-hosseini/AutoGaitA/
 Author: Mahan Hosseini

{autogaita-1.3.1 → autogaita-1.4.0}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.3.1
+Version: 1.4.0
 Summary: Automatic Gait Analysis in Python. A toolbox to streamline and standardise the analysis of kinematics across species after ML-based body posture tracking. Despite being optimised for gait analyses, AutoGaitA has the potential to be used for any kind of kinematic analysis.
 Home-page: https://github.com/mahan-hosseini/AutoGaitA/
 Author: Mahan Hosseini

{autogaita-1.3.1 → autogaita-1.4.0}/autogaita.egg-info/SOURCES.txt

@@ -12,7 +12,6 @@ autogaita/batchrun_scripts/__init__.py
 autogaita/batchrun_scripts/dlc_multirun.py
 autogaita/batchrun_scripts/dlc_singlerun.py
 autogaita/batchrun_scripts/group_dlcrun.py
-autogaita/batchrun_scripts/group_dlcrun_forpaper.py
 autogaita/batchrun_scripts/group_universal3Drun.py
 autogaita/batchrun_scripts/sleap_singlerun.py
 autogaita/batchrun_scripts/universal3D_multirun.py

{autogaita-1.3.1 → autogaita-1.4.0}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.3.1",  # rc == release candidate (before release is finished)
+    version="1.4.0",  # rc == release candidate (before release is finished)
     author="Mahan Hosseini",
     description="Automatic Gait Analysis in Python. A toolbox to streamline and standardise the analysis of kinematics across species after ML-based body posture tracking. Despite being optimised for gait analyses, AutoGaitA has the potential to be used for any kind of kinematic analysis.",
     packages=find_packages(),

autogaita-1.3.1/autogaita/batchrun_scripts/group_dlcrun_forpaper.py

@@ -1,151 +0,0 @@
-import autogaita
-
-
-def group_dlcrun():
-    """
-    Batchrun script to run AutoGaitA Group for Results obtained with AutoGaitA DLC.
-    folderinfo & cfg dictionaries must be configured as explained in our documentation. See the "AutoGaitA without the GUI" section of our documentation for references to in-depth explanations to all dictionary keys (note that each key of dicts corresponds to some object in the AutoGaitA Group GUI)
-    """
-
-    # ----------------------------- 3 Months 3 Beams --------------------------------
-    # folderinfo = {}
-    # folderinfo["group_names"] = [
-    #     # RM Dataset
-    #     "3m_5mm",
-    #     "3m_12mm",
-    #     "3m_25mm",
-    # ]
-    # folderinfo["group_dirs"] = [
-    #     "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/9w/",
-    #     "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/9w/",
-    #     "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/25mm/9w/",
-    # ]
-    # folderinfo["results_dir"] = (
-    #     "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/3Months3BeamsForPaper"
-
-    # ----------------------------- Old Young 3 Beams --------------------------------
-    folderinfo = {}
-    folderinfo["group_names"] = [
-        # RM Dataset
-        "3m_5mm",
-        "3m_12mm",
-        "3m_25mm",
-        "24m_5mm",
-        "24m_12mm",
-        "24m_25mm",
-    ]
-    folderinfo["group_dirs"] = [
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/9w/",
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/9w/",
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/25mm/9w/",
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/104w/",
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/104w/",
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/255mm/104w/",
-    ]
-    folderinfo["results_dir"] = (
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/YoungOld3BeamsForPaper_v2"
-    )
-    folderinfo["load_dir"] = ""
-
-    # cfg
-    cfg = {}
-    cfg["do_permtest"] = False
-    cfg["do_anova"] = True
-    cfg["permutation_number"] = 10000
-    cfg["PCA_n_components"] = 3
-    # cfg["PCA_n_components"] = 0.33
-    # cfg["PCA_custom_scatter_PCs"] = "4,5,6;4,5;2,4,6"
-    cfg["PCA_custom_scatter_PCs"] = ""
-    cfg["PCA_save_3D_video"] = False  # True
-    cfg["PCA_bins"] = ""  # "0-10,24,50-75"
-    cfg["stats_threshold"] = 0.05
-    cfg["plot_SE"] = True
-    cfg["color_palette"] = "Set2"
-    cfg["dont_show_plots"] = True
-    cfg["legend_outside"] = True
-    cfg["which_leg"] = "left"
-    cfg["anova_design"] = "RM ANOVA"
-    cfg["PCA_variables"] = [
-        "Nose x",
-        "Nose y",
-        "Ear base x",
-        "Ear base y",
-        "Front paw tao x",
-        "Front paw tao y",
-        "Wrist x",
-        "Wrist y",
-        "Elbow x",
-        "Elbow y",
-        "Lower Shoulder x",
-        "Lower Shoulder y",
-        "Upper Shoulder x",
-        "Upper Shoulder y",
-        "Iliac Crest x",
-        "Iliac Crest y",
-        "Hip x",
-        "Hip y",
-        "Knee x",
-        "Knee y",
-        "Ankle x",
-        "Ankle y",
-        "Hind paw tao x",
-        "Hind paw tao y",
-        "Tail base y",
-        "Tail center x",
-        "Tail center y",
-        "Tail tip x",
-        "Tail tip y",
-        "Hind paw tao Velocity",
-        "Hind paw tao Acceleration",
-        "Ankle Velocity",
-        "Ankle Acceleration",
-        "Knee Velocity",
-        "Knee Acceleration",
-        "Hip Velocity",
-        "Hip Acceleration",
-        "Iliac Crest Velocity",
-        "Iliac Crest Acceleration",
-        "Ankle Angle",
-        "Knee Angle",
-        "Hip Angle",
-        "Wrist Angle",
-        "Elbow Angle",
-        "Lower Shoulder Angle",
-        "Iliac Crest Angle",
-        "Ankle Angle Velocity",
-        "Ankle Angle Acceleration",
-        "Knee Angle Acceleration",
-        "Hip Angle Velocity",
-        "Hip Angle Acceleration",
-        "Wrist Angle Velocity",
-        "Wrist Angle Acceleration",
-        "Elbow Angle Velocity",
-        "Elbow Angle Acceleration",
-        "Lower Shoulder Angle Velocity",
-        "Lower Shoulder Angle Acceleration",
-        "Iliac Crest Angle Velocity",
-        "Iliac Crest Angle Acceleration",
-    ]
-    cfg["stats_variables"] = [
-        "Hip x",
-        "Hip y",
-        "Knee x",
-        "Knee y",
-        "Ankle x",
-        "Ankle y",
-        "Hind paw tao x",
-        "Hind paw tao y",
-        "Hind paw tao Velocity",
-        "Ankle Velocity",
-        "Knee Velocity",
-        "Ankle Angle",
-        "Knee Angle",
-        "Hip Angle",
-    ]
-    # run
-    autogaita.group(folderinfo, cfg)
-
-
-# %% what happens if we just hit run
-if __name__ == "__main__":
-    group_dlcrun()