autogaita 1.0.6__tar.gz → 1.0.7__tar.gz

{autogaita-1.0.6 → autogaita-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.6
+Version: 1.0.7
 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-1.0.7}/autogaita/batchrun_scripts/group_dlcrun.py

@@ -42,20 +42,17 @@ def group_dlcrun():
         "/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/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/"
     )
-    folderinfo["load_dir"] = (
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
-        # ""
-    )
+    folderinfo["load_dir"] = ""
     # cfg
     cfg = {}
-    cfg["do_permtest"] = True
+    cfg["do_permtest"] = False  # True
     cfg["do_anova"] = True
     cfg["permutation_number"] = 100
-    cfg["PCA_n_components"] = 3
+    cfg["PCA_n_components"] = 6
     # cfg["PCA_n_components"] = 0.33
     # cfg["PCA_custom_scatter_PCs"] = "4,5,6;4,5;2,4,6"
     cfg["PCA_custom_scatter_PCs"] = ""
@@ -71,23 +68,7 @@ def group_dlcrun():
     # 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",
+        # "Hind paw tao y",
         # "Ankle y",
         # "Knee y",
         # "Ankle Angle",
@@ -101,6 +82,22 @@ def group_dlcrun():
         # "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-1.0.6/autogaita/batchrun_scripts/group_universal3Drun_backup.py → autogaita-1.0.7/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -29,8 +29,6 @@ def group_universal3Drun():
         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-1.0.6 → autogaita-1.0.7}/autogaita/common2D/common2D_3_analysis.py

@@ -63,9 +63,6 @@ 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 = (
@@ -184,20 +181,20 @@ 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_stand_step = add_features(step_copy, cfg)
-        return non_stand_step
+        non_norm_step = add_features(step_copy, cfg)
+        return non_norm_step
         # else standardise x (horizontal dimension) at step-cycle level too
     else:
-        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")]
+        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")]
         # note the [0] here is important because it's still a list of len=1!!
-        min_x_standardisation_joint = x_stand_step[
+        min_x_standardisation_joint = x_norm_step[
             cfg["x_standardisation_joint"][0] + "x"
         ].min()
-        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
+        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
 
 
 def add_features(step, cfg):

{autogaita-1.0.6 → autogaita-1.0.7}/autogaita/group/group_3_PCA.py

@@ -218,8 +218,6 @@ def run_PCA(PCA_df, features, cfg):
     # excel files)
     x = pd.DataFrame(x, columns=features)
     # NOTE that this next line changes the PCA_model variable!
-    # pdb.set_trace()
-    x.fillna(0, inplace=True)
     PCs = PCA_model.fit_transform(x)
     # NOTE! we use number_of_PCs from here onwards (in info/plots/etc) to differentiate
     #       between n_components which can be smaller than 1!

autogaita-1.0.7/autogaita/gui/group_gui_config.json

@@ -0,0 +1,42 @@
+[
+    {
+        "group_names": [
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "group_dirs": [
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "results_dir": "",
+        "load_dir": ""
+    },
+    {
+        "do_permtest": true,
+        "do_anova": false,
+        "anova_design": "RM ANOVA",
+        "permutation_number": "10000",
+        "stats_threshold": "0.05",
+        "which_leg": "right",
+        "PCA_n_components": "3",
+        "PCA_custom_scatter_PCs": "",
+        "PCA_save_3D_video": false,
+        "PCA_bins": "",
+        "plot_SE": false,
+        "color_palette": "Set2",
+        "dont_show_plots": false,
+        "legend_outside": true,
+        "stats_variables": [
+        ],
+        "PCA_variables": [
+        ]
+    }
+]

{autogaita-1.0.6 → autogaita-1.0.7}/autogaita/gui/universal3D_gui_config.json

@@ -1,15 +1,15 @@
 [
     {
         "name": "",
-        "root_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/crawling/",
-        "sctable_filename": "Crawling Annotation Table",
-        "postname_flag": true,
-        "postname_string": " - crawling_renamed"
+        "root_dir": "",
+        "sctable_filename": "",
+        "postname_flag": false,
+        "postname_string": ""
     },
     {
         "analyse_singlerun": false,
-        "sampling_rate": "120",
-        "dont_show_plots": true,
+        "sampling_rate": "",
+        "dont_show_plots": false,
         "y_acceleration": true,
         "angular_acceleration": true,
         "bin_num": "25",
@@ -30,37 +30,34 @@
         "legend_outside": true,
         "results_dir": "",
         "joints": [
-            "Foot",
+            "Midfoot",
             "Ankle ",
             "Knee ",
             "Hip ",
-            "Pelvis ",
-            "Shoulder",
-            "Head"
+            "Pelvis "
         ],
         "angles": {
             "name": [
                 "Ankle",
                 "Knee",
-                "Elbow"
+                "Hip"
             ],
             "lower_joint": [
-                "Foot",
+                "Midfoot",
                 "Ankle",
-                "Wrist"
+                "Knee"
             ],
             "upper_joint": [
                 "Knee",
                 "Hip",
-                "Shoulder"
+                "Pelvis"
             ]
         },
-        "fileprep_root_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/walking/",
-        "fileprep_filetype": "xlsx",
-        "fileprep_postname_string": "Subject_",
-        "fileprep_results_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/walking/",
-        "fileprep_separator": "_",
-        "fileprep_string_to_remove": "",
-        "fileprep_3D_DLC": false
+        "fileprep_root_dir": "",
+        "fileprep_filetype": "",
+        "fileprep_postname_string": "",
+        "fileprep_results_dir": "",
+        "fileprep_separator": "",
+        "fileprep_string_to_remove": ""
     }
 ]

{autogaita-1.0.6 → autogaita-1.0.7}/autogaita/universal3D/universal3D_3_analysis.py

@@ -35,7 +35,7 @@ from autogaita.universal3D.universal3D_constants import (
 # 3) we then we flip y columns if needed (to simulate equal walking direction)
 # 4) immediately after 3 & 4 and for each step's data separately, we compute and add
 #    features (angles, velocities, accelerations)
-#    ==> see standardise_y_z_and_add_features_to_one_step & helper functions a
+#    ==> see norm_z_flip_y_and_add_features_to_one_step & helper functions a
 # 5) immediately after adding features, we normalise a step to bin_num
 #    ==> see normalise_one_steps_data & helper functions b
 # 6) we add original and normalised steps to all_steps_data and normalised_steps_data
@@ -56,7 +56,6 @@ def analyse_and_export_stepcycles(data, all_cycles, global_Y_max, info, cfg):
     results_dir = info["results_dir"]
     bin_num = cfg["bin_num"]
     analyse_average_y = cfg["analyse_average_y"]
-    standardise_y_coordinates = cfg["standardise_y_coordinates"]
     # do everything on a copy of the data df
     data_copy = data.copy()
     # for exports, we don't need all_cycles to be separated for runs
@@ -66,7 +65,6 @@ def analyse_and_export_stepcycles(data, all_cycles, global_Y_max, info, cfg):
     delete_previous_xlsfiles(name, results_dir)
     # initialise list of dfs & results
     all_steps_data = [pd.DataFrame(data=None)] * len(OUTPUTS)
-    y_standardised_steps_data = [pd.DataFrame(data=None)] * len(OUTPUTS)
     normalised_steps_data = [pd.DataFrame(data=None)] * len(OUTPUTS)
     average_data = [pd.DataFrame(data=None)] * len(OUTPUTS)
     std_data = [pd.DataFrame(data=None)] * len(OUTPUTS)
@@ -75,74 +73,38 @@ def analyse_and_export_stepcycles(data, all_cycles, global_Y_max, info, cfg):
     # .................  loop over legs and populate dfs  ..............................
     # for each step:
     # 1) extract it from data_copy (this_step)
-    # 2) normalise z if wanted
-    # 3) standardise y to a joint if wanted
-    # 4) flip y columns if wanted
-    # 5) add features
-    # 6) normalise its length to bin_num (this_normalised_step)
-    # 7) add this_step to all_steps_data, this_normalised_step to
-    #    normalised_steps_data and this_x_standardised_step to x_standardised_steps_data
+    # 2) normalise Z if wanted, flip y columns if needed and add features
+    # 3) normalise its length to bin_num (this_normalised_step)
+    # 4) add this_step to all_steps_data and this_normalised_step to
+    #    normalised_steps_data
     for l_idx, legname in enumerate(LEGS):
         # 1 step only (highly unlikely in humans)
         if len(all_cycles[legname]) == 1:
             this_step = data_copy.loc[
                 all_cycles[legname][0][0] : all_cycles[legname][0][1]
             ]
-            if standardise_y_coordinates:
-                this_step, y_standardised_step = (
-                    standardise_y_z_and_add_features_to_one_step(
-                        this_step, global_Y_max, cfg
-                    )
-                )
-                all_steps_data[l_idx] = this_step
-                y_standardised_steps_data[l_idx] = y_standardised_step
-                normalised_steps_data[l_idx] = normalise_one_steps_data(
-                    y_standardised_step, bin_num
-                )
-            else:
-                this_step = standardise_y_z_and_add_features_to_one_step(
-                    this_step, global_Y_max, cfg
-                )
-                all_steps_data[l_idx] = this_step
-                normalised_steps_data[l_idx] = normalise_one_steps_data(
-                    this_step, bin_num
-                )
+            this_step = norm_z_flip_y_and_add_features_to_one_step(
+                this_step, global_Y_max, cfg
+            )
+            all_steps_data[l_idx] = this_step
+            normalised_steps_data[l_idx] = normalise_one_steps_data(this_step, bin_num)
             sc_num[l_idx] = 1
         # 2 or more steps - build dataframes
         elif len(all_cycles[legname]) > 1:
             # first step is added manually
-            # NOTE
-            # ----
-            # normalised_steps_data is created using y_standardised_step or first_step
             first_step = data_copy.loc[
                 all_cycles[legname][0][0] : all_cycles[legname][0][1]
             ]
-            if standardise_y_coordinates:
-                first_step, y_standardised_first_step = (
-                    standardise_y_z_and_add_features_to_one_step(
-                        first_step, global_Y_max, cfg
-                    )
-                )
-                all_steps_data[l_idx] = first_step
-                normalised_steps_data[l_idx] = normalise_one_steps_data(
-                    y_standardised_first_step, bin_num
-                )
-            else:
-                first_step = standardise_y_z_and_add_features_to_one_step(
-                    first_step, global_Y_max, cfg
-                )
-                all_steps_data[l_idx] = first_step
-                normalised_steps_data[l_idx] = normalise_one_steps_data(
-                    first_step, bin_num
-                )
+            first_step = norm_z_flip_y_and_add_features_to_one_step(
+                first_step, global_Y_max, cfg
+            )
+            all_steps_data[l_idx] = first_step
+            normalised_steps_data[l_idx] = normalise_one_steps_data(first_step, bin_num)
             # some prep for addition of further steps
             sc_num[l_idx] = len(all_cycles[legname])
             nanvector = data_copy.loc[[SEPARATOR_IDX]]
             nanvector[:] = np.nan
             # .............................  step-loop  ................................
-
-            # STOPPED IMPLEMENTING Y-STANDARDISATION HERE
-
             for s in range(1, sc_num[l_idx], 1):
                 # get step separators
                 numvector = data_copy.loc[[SEPARATOR_IDX]]
@@ -154,7 +116,7 @@ def analyse_and_export_stepcycles(data, all_cycles, global_Y_max, info, cfg):
                 this_step = data_copy.loc[
                     all_cycles[legname][s][0] : all_cycles[legname][s][1]
                 ]
-                this_step = standardise_y_z_and_add_features_to_one_step(
+                this_step = norm_z_flip_y_and_add_features_to_one_step(
                     this_step, global_Y_max, cfg
                 )
                 all_steps_data[l_idx] = pd.concat(
@@ -264,15 +226,15 @@ def analyse_and_export_stepcycles(data, all_cycles, global_Y_max, info, cfg):
 # ......................................................................................
 
 
-def standardise_y_z_and_add_features_to_one_step(step, global_Y_max, cfg):
-    """For a single step cycle's data, standardise y & z if wanted, flip y columns if wanted (to simulate equal run direction) and add features (angles & velocities)"""
+def norm_z_flip_y_and_add_features_to_one_step(step, global_Y_max, cfg):
+    """For a single step cycle's data, normalise z if wanted, flip y columns if needed
+    (to simulate equal run direction) and add features (angles & velocities)
+    """
     # unpack
     standardise_z_at_SC_level = cfg["standardise_z_at_SC_level"]
     standardise_z_to_a_joint = cfg["standardise_z_to_a_joint"]
     z_standardisation_joint = cfg["z_standardisation_joint"]
     flip_gait_direction = cfg["flip_gait_direction"]
-    standardise_y_coordinates = cfg["standardise_y_coordinates"]
-    y_standardisation_joint = cfg["y_standardisation_joint"]
     direction_joint = cfg["direction_joint"]
     # if user wanted this, normalise z (height) at step-cycle level
     step_copy = step.copy()
@@ -284,51 +246,15 @@ def standardise_y_z_and_add_features_to_one_step(step, global_Y_max, cfg):
         else:
             z_minimum = min(step_copy[z_cols].min())
         step_copy[z_cols] -= z_minimum
-    # no y-standardisation, just flip the step if needed, add features and return
-    if standardise_y_coordinates is False:
-        non_stand_step = step_copy.copy()
-        if flip_gait_direction:
-            non_stand_step = flip_a_steps_gait_direction(
-                non_stand_step, direction_joint, global_Y_max
-            )
-        non_stand_step = add_features(non_stand_step, cfg)
-        return non_stand_step
-
-    # user wanted y-standardisation, make sure that we do this before gait flipping!
-    # => i.e. flip gait direction and add features for both, non_stand & y_stand steps
-    # IMPORTANT
-    # ---------
-    # Y-standardising to the MINIMUM of the chosen joint is correct because of flipping
-    # y columns in flip_a_steps_gait_direction if the first idx of the step's direction
-    # joint is higher than its average value
-    # therefore y is always increasing as the step progresses and thus it is correct
-    # that we standardise to the minimum via subtraction as we do here
-    else:
-        non_stand_step = step_copy.copy()
-        y_stand_step = step_copy.copy()
-        y_cols = [col for col in y_stand_step.columns if col.endswith("Y")]
-        # note the [0] here is important because it's still a list of len=1!
-        y_minimum = y_stand_step[y_standardisation_joint[0] + "Y"].min()
-        y_stand_step[y_cols] -= y_minimum
-        if flip_gait_direction:
-            non_stand_step = flip_a_steps_gait_direction(
-                non_stand_step, direction_joint, global_Y_max
-            )
-            y_stand_step = flip_a_steps_gait_direction(
-                y_stand_step, direction_joint, global_Y_max
-            )
-        non_stand_step = add_features(non_stand_step, cfg)
-        y_stand_step = add_features(y_stand_step, cfg)
-        return non_stand_step, y_stand_step
-
-
-def flip_a_steps_gait_direction(step, direction_joint, global_Y_max):
-    """Flip a step's y cols checking if needed with direction joint"""
-    direction_joint_col_idx = step.columns.get_loc(direction_joint)
-    direction_joint_mean = np.mean(step[direction_joint])
-    if step.iloc[0, direction_joint_col_idx] > direction_joint_mean:
-        step = flip_y_columns(step, global_Y_max)
-    return step
+    # if user wanted flipping & if we need to flip y cols of this given step do so
+    if flip_gait_direction:
+        direction_joint_col_idx = step_copy.columns.get_loc(direction_joint)
+        direction_joint_mean = np.mean(step_copy[direction_joint])
+        if step_copy.iloc[0, direction_joint_col_idx] > direction_joint_mean:
+            step_copy = flip_y_columns(step_copy, global_Y_max)
+    # add angles and velocities
+    step_copy = add_features(step_copy, cfg)
+    return step_copy
 
 
 def flip_y_columns(step, global_Y_max):

{autogaita-1.0.6 → autogaita-1.0.7}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.6
+Version: 1.0.7
 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-1.0.7}/autogaita.egg-info/SOURCES.txt

@@ -12,9 +12,7 @@ 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/group_universal3Drun_backup.py
 autogaita/batchrun_scripts/sleap_singlerun.py
 autogaita/batchrun_scripts/universal3D_multirun.py
 autogaita/batchrun_scripts/universal3D_singlerun.py

{autogaita-1.0.6 → autogaita-1.0.7}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.0.6",  # rc == release candidate (before release is finished)
+    version="1.0.7",  # 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-1.0.6/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()

autogaita-1.0.6/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -1,139 +0,0 @@
-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-1.0.6/autogaita/gui/group_gui_config.json

@@ -1,121 +0,0 @@
-[
-    {
-        "group_names": [
-            "crawling",
-            "sideways",
-            "walking",
-            "jogging",
-            "jumping_jack",
-            "vertical_jumping"
-        ],
-        "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/"
-        ],
-        "results_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/First Analysis/gaita prepared/gaita_tests/",
-        "load_dir": ""
-    },
-    {
-        "do_permtest": true,
-        "do_anova": true,
-        "anova_design": "RM ANOVA",
-        "permutation_number": "10000",
-        "stats_threshold": "0.05",
-        "which_leg": "left",
-        "PCA_n_components": "10",
-        "PCA_custom_scatter_PCs": "",
-        "PCA_save_3D_video": true,
-        "PCA_bins": "",
-        "plot_SE": false,
-        "color_palette": "Set2",
-        "dont_show_plots": false,
-        "legend_outside": true,
-        "stats_variables": [],
-        "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"
-        ]
-    }
-]