autogaita 1.0.4__tar.gz → 1.0.6__tar.gz

{autogaita-1.0.4 → autogaita-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.4
+Version: 1.0.6
 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-1.0.6/autogaita/batchrun_scripts/group_dlcrun.py

@@ -0,0 +1,112 @@
+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)
+    """
+    # folderinfo
+    # => Note that length of folderinfo's group_names & group_dirs lists determines how #    many groups are compared.
+    # => Also note that indices must correspond (i.e., idx #    1's name will be used #    for dataset stored in group_dir's idx 1)
+    folderinfo = {}
+    folderinfo["group_names"] = [
+        # RM Dataset
+        "5mm",
+        "12mm",
+        "25mm",
+        # Interaction Issue Dataset
+        # "Control",
+        # "Silenced",
+        # Testing Dataset
+        # "one",
+        # "two",
+    ]
+    folderinfo["group_dirs"] = [
+        # --------------------------
+        # Full Dataset (39 subjects)
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control Full",
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced Full/",
+        # --------------------------
+        # Reduced Dataset (5 subjects)
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control",
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced/",
+        # --------------------------
+        # Testing Dataset
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 1/",
+        # "/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/",
+    ]
+    folderinfo["results_dir"] = (
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results5/"
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Mahan Results/"
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/GroupResults/"
+    )
+    folderinfo["load_dir"] = (
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
+        # ""
+    )
+    # cfg
+    cfg = {}
+    cfg["do_permtest"] = True
+    cfg["do_anova"] = True
+    cfg["permutation_number"] = 100
+    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"] = False
+    cfg["color_palette"] = "viridis"
+    cfg["dont_show_plots"] = True
+    cfg["legend_outside"] = True
+    cfg["which_leg"] = "left"
+    cfg["anova_design"] = "RM ANOVA"
+    # cfg["anova_design"] = "Mixed ANOVA"
+    cfg["permutation_number"] = 100
+    cfg["PCA_variables"] = [
+        "Hind paw tao y",
+        "Ankle y",
+        "Knee y",
+        "Ankle Angle",
+        "Knee Angle",
+        "Nose x",
+        "Knee y",
+        "Knee x",
+        "Knee Velocity",
+        "Knee Acceleration",
+        "Knee Angle",
+        "Knee Angle Velocity",
+        "Knee Angle Acceleration",
+        "Hip Angle",
+    ]
+    cfg["stats_variables"] = [
+        "Hind paw tao y",
+        # "Ankle y",
+        # "Knee y",
+        # "Ankle Angle",
+        # "Knee Angle",
+        # "Nose x",
+        # "Knee y",
+        # "Knee x",
+        # "Knee Velocity",
+        # "Knee Acceleration",
+        # "Knee Angle",
+        # "Knee Angle Velocity",
+        # "Knee Angle Acceleration",
+        # "Hip Angle",
+        # "Elbow Angle"
+    ]
+    # run
+    autogaita.group(folderinfo, cfg)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    group_dlcrun()

autogaita-1.0.6/autogaita/batchrun_scripts/group_dlcrun_forpaper.py

@@ -0,0 +1,151 @@
+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()

autogaita-1.0.6/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -0,0 +1,139 @@
+import autogaita
+
+
+def group_universal3Drun():
+    """
+    Batchrun script to run AutoGaitA Group for Results obtained with AutoGaitA Universal 3D.
+    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)
+    """
+    # loop over legs - currently no option to do both legs in a single run
+    cfg = {}
+    # folderinfo
+    # => Note that length of folderinfo's group_names & group_dirs lists determines #    how many groups are compared.
+    # => Also note that indices must correspond (i.e., idx #    1's name will be #    used for dataset stored in group_dir's idx 1)
+    folderinfo = {}
+    folderinfo["group_names"] = [
+        "crawling",
+        "sideways",
+        "walking",
+        "jogging",
+        "jumping_jack",
+        "vertical_jumping",
+    ]
+    folderinfo["group_dirs"] = [
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/crawling/Results/",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/sideways/Results/",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/walking/Results/",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/jogging/Results/",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/jumping_jack/Results/",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/vertical_jumping/Results/",
+    ]
+    folderinfo["results_dir"] = (
+        "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/group/"
+    )
+    folderinfo["load_dir"] = ""
+    # cfg
+    cfg["do_permtest"] = True
+    cfg["do_anova"] = True
+    cfg["permutation_number"] = 10000
+    cfg["PCA_n_components"] = 10
+    cfg["PCA_custom_scatter_PCs"] = ""
+    cfg["PCA_save_3D_video"] = True
+    cfg["PCA_bins"] = ""
+    cfg["stats_threshold"] = 0.05
+    cfg["plot_SE"] = False
+    cfg["color_palette"] = "Set2"
+    cfg["legend_outside"] = True
+    cfg["dont_show_plots"] = True
+    cfg["anova_design"] = "Mixed ANOVA"
+    cfg["which_leg"] = "right"
+    cfg["PCA_variables"] = [
+        "Head Y",
+        "Head Z",
+        "Hip Y",
+        "Hip Z",
+        "Pelvis Y",
+        "Pelvis Z",
+        "Thorax Y",
+        "Thorax Z",
+        "Ankle, left Y",
+        "Ankle, left Z",
+        "Elbow, left Y",
+        "Elbow, left Z",
+        "Hip, left Y",
+        "Hip, left Z",
+        "Hand, left Y",
+        "Hand, left Z",
+        "Knee, left Y",
+        "Knee, left Z",
+        "Shoulder, left Y",
+        "Shoulder, left Z",
+        "Wrist, left Y",
+        "Wrist, left Z",
+        "Foot, left Y",
+        "Foot, left Z",
+        "Ankle, right Y",
+        "Ankle, right Z",
+        "Elbow, right Y",
+        "Elbow, right Z",
+        "Hip, right Y",
+        "Hip, right Z",
+        "Hand, right Y",
+        "Hand, right Z",
+        "Knee, right Y",
+        "Knee, right Z",
+        "Shoulder, right Y",
+        "Shoulder, right Z",
+        "Wrist, right Y",
+        "Wrist, right Z",
+        "Foot, right Y",
+        "Foot, right Z",
+        "Ankle, left Angle",
+        "Knee, left Angle",
+        "Elbow, left Angle",
+        "Foot, left Velocity",
+        "Foot, left Acceleration",
+        "Ankle, left Velocity",
+        "Ankle, left Acceleration",
+        "Knee, left Velocity",
+        "Knee, left Acceleration",
+        "Hip Velocity",
+        "Hip Acceleration",
+        "Pelvis Velocity",
+        "Pelvis Acceleration",
+        "Shoulder, left Velocity",
+        "Shoulder, left Acceleration",
+        "Head Velocity",
+        "Head Acceleration",
+        "Ankle, left Angle Velocity",
+        "Ankle, left Angle Acceleration",
+        "Knee, left Angle Velocity",
+        "Knee, left Angle Acceleration",
+        "Elbow, left Angle Velocity",
+        "Elbow, left Angle Acceleration",
+        "Ankle, right Angle",
+        "Knee, right Angle",
+        "Elbow, right Angle",
+        "Foot, right Velocity",
+        "Foot, right Acceleration",
+        "Ankle, right Velocity",
+        "Ankle, right Acceleration",
+        "Knee, right Velocity",
+        "Knee, right Acceleration",
+        "Shoulder, right Velocity",
+        "Shoulder, right Acceleration",
+        "Ankle, right Angle Velocity",
+        "Ankle, right Angle Acceleration",
+        "Knee, right Angle Velocity",
+        "Knee, right Angle Acceleration",
+        "Elbow, right Angle Velocity",
+        "Elbow, right Angle Acceleration",
+    ]
+    cfg["stats_variables"] = []
+    # run
+    autogaita.group(folderinfo, cfg)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    group_universal3Drun()

autogaita-1.0.4/autogaita/batchrun_scripts/group_universal3Drun.py → autogaita-1.0.6/autogaita/batchrun_scripts/group_universal3Drun_backup.py

@@ -23,11 +23,14 @@ def group_universal3Drun():
             + cfg["which_leg"]
             + " leg/"
         )
+        folderinfo["load_dir"] = ""
         # cfg
         cfg["do_permtest"] = True
         cfg["do_anova"] = True
         cfg["permutation_number"] = 10
         cfg["PCA_n_components"] = 3
+        cfg["PCA_custom_scatter_PCs"] = ""
+        cfg["PCA_bins"] = ""
         cfg["PCA_save_3D_video"] = False
         cfg["stats_threshold"] = 0.05
         cfg["plot_SE"] = False

{autogaita-1.0.4 → autogaita-1.0.6}/autogaita/batchrun_scripts/universal3D_multirun.py

@@ -24,11 +24,16 @@ def universal3D_multirun():
     cfg["angular_acceleration"] = True
     cfg["bin_num"] = 25
     cfg["plot_SE"] = True
-    cfg["normalise_height_at_SC_level"] = True
+    cfg["standardise_z_at_SC_level"] = True
+    cfg["standardise_z_to_a_joint"] = True
+    cfg["z_standardisation_joint"] = ["Foot, left"]
     cfg["plot_joint_number"] = 7
     cfg["color_palette"] = "viridis"
     cfg["legend_outside"] = True
+    cfg["flip_gait_direction"] = False
     cfg["analyse_average_y"] = True
+    cfg["standardise_y_coordinates"] = True
+    cfg["y_standardisation_joint"] = ["Foot"]
     cfg["joints"] = ["Midfoot", "Ankle", "Knee", "Hip", "Pelvis", "Shoulder", "Neck"]
     cfg["angles"] = {
         "name": ["Ankle", "Knee"],

{autogaita-1.0.4 → autogaita-1.0.6}/autogaita/batchrun_scripts/universal3D_singlerun.py

@@ -23,11 +23,16 @@ def universal3D_singlerun():
     cfg["angular_acceleration"] = True
     cfg["bin_num"] = 25
     cfg["plot_SE"] = True
-    cfg["normalise_height_at_SC_level"] = True
+    cfg["standardise_z_at_SC_level"] = True
+    cfg["standardise_z_to_a_joint"] = True
+    cfg["z_standardisation_joint"] = ["Midfoot"]
     cfg["plot_joint_number"] = 5
     cfg["color_palette"] = "Set2"
     cfg["legend_outside"] = True
-    cfg["analyse_average_y"] = False
+    cfg["flip_gait_direction"] = False
+    cfg["analyse_average_y"] = True
+    cfg["standardise_y_coordinates"] = True
+    cfg["y_standardisation_joint"] = ["Midfoot"]
     cfg["joints"] = [
         # "R1-ThCx",
         "Midfoot",

{autogaita-1.0.4 → autogaita-1.0.6}/autogaita/common2D/common2D_3_analysis.py

@@ -63,6 +63,9 @@ def analyse_and_export_stepcycles(data, all_cycles, info, cfg):
     # 2 or more steps - build dataframe
     elif len(all_cycles) > 1:
         # first- step is added manually
+        # NOTE
+        # ----
+        # normalised_steps_data is created using x_standardised_steps_data or first_step
         first_step = data_copy.loc[all_cycles[0][0] : all_cycles[0][1]]
         if standardise_x_coordinates:
             all_steps_data, x_standardised_steps_data = (
@@ -181,20 +184,20 @@ def standardise_x_y_and_add_features_to_one_step(step, cfg):
         step_copy[y_cols] -= this_y_min
     # if no x-standardisation, just add features & return non-(x-)normalised step
     if cfg["standardise_x_coordinates"] is False:
-        non_norm_step = add_features(step_copy, cfg)
-        return non_norm_step
+        non_stand_step = add_features(step_copy, cfg)
+        return non_stand_step
         # else standardise x (horizontal dimension) at step-cycle level too
     else:
-        non_norm_step = add_features(step_copy, cfg)
-        x_norm_step = step_copy.copy()
-        x_cols = [col for col in x_norm_step.columns if col.endswith("x")]
+        non_stand_step = add_features(step_copy, cfg)
+        x_stand_step = step_copy.copy()
+        x_cols = [col for col in x_stand_step.columns if col.endswith("x")]
         # note the [0] here is important because it's still a list of len=1!!
-        min_x_standardisation_joint = x_norm_step[
+        min_x_standardisation_joint = x_stand_step[
             cfg["x_standardisation_joint"][0] + "x"
         ].min()
-        x_norm_step[x_cols] -= min_x_standardisation_joint
-        x_norm_step = add_features(x_norm_step, cfg)
-        return non_norm_step, x_norm_step
+        x_stand_step[x_cols] -= min_x_standardisation_joint
+        x_stand_step = add_features(x_stand_step, cfg)
+        return non_stand_step, x_stand_step
 
 
 def add_features(step, cfg):

{autogaita-1.0.4 → autogaita-1.0.6}/autogaita/dlc/dlc_1_preparation.py

@@ -169,7 +169,7 @@ def some_prep(info, folderinfo, cfg):
     beam_hind_jointadd = cfg["beam_hind_jointadd"]
     beam_fore_jointadd = cfg["beam_fore_jointadd"]
     direction_joint = cfg["direction_joint"]
-    # important to unpack to vars hand not to cfg since cfg is overwritten in multiruns!
+    # important to unpack to vars and not to cfg since cfg is overwritten in multiruns!
     x_standardisation_joint = cfg["x_standardisation_joint"][0]
     y_standardisation_joint = cfg["y_standardisation_joint"][0]
     # store config json file @ group path

{autogaita-1.0.4 → autogaita-1.0.6}/autogaita/group/group_1_preparation.py

@@ -49,43 +49,59 @@ def some_prep(folderinfo, cfg):
         if os.path.exists(info_file_path):
             os.remove(info_file_path)
 
-    # extracted_cfg_vars: save_to_xls, PCA stuff & dont show plots
-    cfg = extract_cfg_vars(folderinfo, cfg)
-
-    # see if there's a config json file and add to cfg dict
-    for g_idx, group_dir in enumerate(group_dirs):
+    # *********** IMPORTANT ***********
+    # if load_dir, we have already saved a group config.json (see below before return)
+    # => use this and just return the cfg
+    # => make sure to write folderinfo["contrast"] manually above as is and then return
+    #    that folderinfo plus the cfg you load from the file
+    if len(folderinfo["load_dir"]) > 0:
         with open(
-            os.path.join(group_dir, CONFIG_JSON_FILENAME), "r"
+            os.path.join(folderinfo["load_dir"], CONFIG_JSON_FILENAME), "r"
         ) as config_json_file:
-            config_vars_from_json = json.load(config_json_file)
-            for key in config_vars_from_json.keys():
-                # assigning like this ensure all keys are in all jsons across groups
-                if g_idx == 0:
-                    cfg[key] = config_vars_from_json[key]
-                else:
-                    # sanity check for group-differences in cfg variables!
-                    if (key not in cfg.keys()) | (
-                        cfg[key] != config_vars_from_json[key]
-                    ):
-                        error_message = (
-                            "config.json variables differ between groups!"
-                            + "\nPlease make sure that all cfg variables between "
-                            + "groups match & try again!"
-                        )
-                        raise ValueError(error_message)
-                    else:
+            cfg = json.load(config_json_file)
+            cfg["loaded"] = True  # used in a unit test in test_group_unit.py
+
+    else:  # if not, do the below things based on group dirs' configs
+        # 1. extracted_cfg_vars: save_to_xls, PCA stuff & dont show plots
+        cfg = extract_cfg_vars(folderinfo, cfg)
+
+        # 2. ennsure each key's across-group-equivalence and then add to cfg dict
+        for g_idx, group_dir in enumerate(group_dirs):
+            with open(
+                os.path.join(group_dir, CONFIG_JSON_FILENAME), "r"
+            ) as config_json_file:
+                config_vars_from_json = json.load(config_json_file)
+                for key in config_vars_from_json.keys():
+                    # assigning like this ensure all keys are in all jsons across groups
+                    if g_idx == 0:
                         cfg[key] = config_vars_from_json[key]
+                    else:
+                        # sanity check for group-differences in cfg variables!
+                        if (key not in cfg.keys()) | (
+                            cfg[key] != config_vars_from_json[key]
+                        ):
+                            error_message = (
+                                "config.json variables differ between groups!"
+                                + "\nPlease make sure that all cfg variables between "
+                                + "groups match & try again!"
+                            )
+                            raise ValueError(error_message)
+                        else:
+                            cfg[key] = config_vars_from_json[key]
 
-    # after having checked cfg keys for equivalence, we have to make sure that
-    # hind_joints is renamed to joints if DLC
-    # => note that cfg will not be updated (and overwritten from input if Universal 3D so it's)
-    #    okay that we do this
-    if cfg["tracking_software"] == "DLC":
-        cfg["joints"] = cfg["hind_joints"]
-    joints = cfg["joints"]
-    angles = cfg["angles"]
+        # 3. rename hind_joints is to joints if DLC or SLEAP
+        if "hind_joints" in cfg.keys():
+            cfg["joints"] = cfg["hind_joints"]
 
-    # prepare some plotting color stuff
+    # ******** IMPORTANT *******
+    # => Do the following two things regardless of load_dir:
+    # 1. save cfg to json file in results_dir for load_dir capability
+    config_json_path = os.path.join(results_dir, CONFIG_JSON_FILENAME)
+    if os.path.exists(config_json_path):  # overwrite if exists
+        os.remove(config_json_path)
+    with open(config_json_path, "w") as config_json_file:
+        json.dump(cfg, config_json_file)
+    # 2. create this plot stuff manually (cycler objects cannot be written to json)
     cfg["group_color_cycler"] = plt.cycler(
         "color", sns.color_palette(cfg["color_palette"], len(group_names))
     )
@@ -93,10 +109,10 @@ def some_prep(folderinfo, cfg):
         zip(group_names, cfg["group_color_cycler"].by_key()["color"])
     )
     cfg["joint_color_cycler"] = plt.cycler(
-        "color", sns.color_palette(cfg["color_palette"], len(joints))
+        "color", sns.color_palette(cfg["color_palette"], len(cfg["joints"]))
     )
     cfg["angle_color_cycler"] = plt.cycler(
-        "color", sns.color_palette(cfg["color_palette"], len(angles["name"]))
+        "color", sns.color_palette(cfg["color_palette"], len(cfg["angles"]["name"]))
     )
 
     return folderinfo, cfg