autogaita 1.0.3__tar.gz → 1.0.4__tar.gz

{autogaita-1.0.3 → autogaita-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.3
+Version: 1.0.4
 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-1.0.3 → autogaita-1.0.4}/autogaita/batchrun_scripts/group_dlcrun.py

@@ -13,9 +13,9 @@ def group_dlcrun():
     folderinfo["group_names"] = [
         # ----------
         # RM Dataset
-        # "5mm",
-        # "12mm",
-        # "25mm",
+        "5mm",
+        "12mm",
+        "25mm",
         # -------
         # Interaction Issue Dataset
         # "Control",
@@ -26,12 +26,12 @@ def group_dlcrun():
         # "two",
         # --------
         # Beam x Age for Manuscript
-        "3m_5mm",
-        "3m_12mm",
-        "3m_25mm",
-        "24m_5mm",
-        "24m_12mm",
-        "24m_25mm",
+    #     "3m_5mm",
+    #     "3m_12mm",
+    #     "3m_25mm",
+    #     "24m_5mm",
+    #     "24m_12mm",
+    #     "24m_25mm",
     ]
     folderinfo["group_dirs"] = [
         # --------------------------
@@ -48,23 +48,23 @@ def group_dlcrun():
         # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 2/",
         # --------------------------
         # RM Dataset (example data in repo)
-        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/5mm/Results/",
-        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/12mm/Results/",
-        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/25mm/Results/",
+        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/5mm/Results/",
+        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/12mm/Results/",
+        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/25mm/Results/",
         # --------------------------
         # Beam x Age for Manuscript
-        "/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 2024/25mm/104w"
+        # "/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 2024/25mm/104w"
     ]
     folderinfo["results_dir"] = (
         # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
         # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Mahan Results/"
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/GroupResults/"
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/YoungOld3BeamsForPaper"
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/GroupResults/"
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/TESTINGBIGDATA/"
     )
     # cfg
     cfg = {}
@@ -85,65 +85,65 @@ def group_dlcrun():
     # cfg["anova_design"] = "Mixed ANOVA"
     cfg["PCA_variables"] = [
         # Beam x Age
-        "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",
+        # "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",
 
 
         # PREVIOUS TESTING FEATURES
@@ -167,7 +167,7 @@ def group_dlcrun():
         # "Hind paw tao y",
         # "Ankle y",
         # "Knee y",
-        # "Ankle Angle",
+        "Ankle Angle",
         # "Knee Angle",
         # "Nose x",
         # "Knee y",
@@ -181,21 +181,21 @@ def group_dlcrun():
         # "Elbow Angle"
 
 
-        # Beam x Age
-        "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"
+        # # Beam x Age
+        # "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)

{autogaita-1.0.3 → autogaita-1.0.4}/autogaita/group/group_4_stats.py

@@ -586,6 +586,8 @@ def ANOVA_main(
     # => note pingouin checks both or sphericity by default
     if just_do_tukeys is False:
         ANOVA_result = run_ANOVA(stats_df, stats_var, cfg)
+    else:
+        ANOVA_result = None
 
     # run Tukeys for pairwise comparisons
     # => always running multiple comparison tests as well. see Prism's doc for why
@@ -995,14 +997,25 @@ def save_stats_summary_to_text(
     message = ""
 
     # only for ANOVA - add the table above contrast loop
-    if "ANOVA" in which_test:
+    if "ANOVA" in which_test and ANOVA_result is not None:
         message = (
             message
             + "\n\n--------------------\nA N O V A  T A B L E"
             + "\n--------------------"
             + "\n"
-            + str(ANOVA_result)
         )
+        message += "\n"  # col header row
+        for col in ANOVA_result.columns:
+            message += f"| {col} | "
+        n_rows, n_cols = np.shape(ANOVA_result)
+        for row_idx in range(n_rows):
+            message += "\n"  # new row
+            for col_idx in range(n_cols):
+                val = ANOVA_result.iloc[row_idx, col_idx]
+                if isinstance(val, str):
+                    message += f"| {val} | "
+                else:
+                    message += f"| {str(round(val, 4))} | "
 
     # contrast specific info
     for contrast in contrasts:

{autogaita-1.0.3 → autogaita-1.0.4}/autogaita/group/group_main.py

@@ -110,17 +110,20 @@ def group(folderinfo, cfg):
                 tukeys_only_info_message(folderinfo)
             else:
                 just_do_tukeys = False
-                for stats_var in cfg["stats_variables"]:
-                    ANOVA_main(
-                        stats_df,
-                        g_avg_dfs,
-                        g_std_dfs,
-                        stats_var,
-                        just_do_tukeys,
-                        folderinfo,
-                        cfg,
-                        plot_panel_instance,
-                    )
+            # this function is called ANOVA_main even though we might just run Tukeys
+            # with it and not exactly an ANOVA as well
+            # => see conditions in sanity check setting just_do_tukeys
+            for stats_var in cfg["stats_variables"]:
+                ANOVA_main(
+                    stats_df,
+                    g_avg_dfs,
+                    g_std_dfs,
+                    stats_var,
+                    just_do_tukeys,
+                    folderinfo,
+                    cfg,
+                    plot_panel_instance,
+                )
         plt.close("all")
 
     # ..................................  plots  .......................................

autogaita-1.0.4/autogaita/gui/group_gui_config.json

@@ -0,0 +1,41 @@
+[
+    {
+        "group_names": [
+            "3m_25mm",
+            "24m_25mm",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "group_dirs": [
+            "/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 2024/25mm/104w",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "results_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/YoungOld25mm/"
+    },
+    {
+        "do_permtest": false,
+        "do_anova": true,
+        "anova_design": "Mixed ANOVA",
+        "permutation_number": "10000",
+        "stats_threshold": "0.05",
+        "which_leg": "right",
+        "PCA_n_components": "3",
+        "PCA_custom_scatter_PCs": "",
+        "PCA_save_3D_video": true,
+        "PCA_bins": "",
+        "plot_SE": true,
+        "color_palette": "Set2",
+        "dont_show_plots": false,
+        "legend_outside": true,
+        "stats_variables": [
+            "Ankle Angle"
+        ],
+        "PCA_variables": []
+    }
+]

{autogaita-1.0.3 → autogaita-1.0.4}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.3
+Version: 1.0.4
 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-1.0.3 → autogaita-1.0.4}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.0.3",  # rc == release candidate (before release is finished)
+    version="1.0.4",  # 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-1.0.3/autogaita/gui/group_gui_config.json

@@ -1,114 +0,0 @@
-[
-    {
-        "group_names": [
-            "3m_5mm",
-            "3m_12mm",
-            "3m_25mm",
-            "",
-            "",
-            ""
-        ],
-        "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",
-            "",
-            "",
-            ""
-        ],
-        "results_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/3m3BeamsForPaper"
-    },
-    {
-        "do_permtest": false,
-        "do_anova": true,
-        "anova_design": "RM ANOVA",
-        "permutation_number": "10000",
-        "stats_threshold": "0.05",
-        "which_leg": "right",
-        "PCA_n_components": "0.9",
-        "PCA_custom_scatter_PCs": "1,3;2,3;2,3,4;",
-        "PCA_save_3D_video": true,
-        "PCA_bins": "",
-        "plot_SE": true,
-        "color_palette": "inferno",
-        "dont_show_plots": false,
-        "legend_outside": true,
-        "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"
-        ],
-        "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"
-        ]
-    }
-]