autogaita 1.5.0__tar.gz → 1.5.1__tar.gz

{autogaita-1.5.0 → autogaita-1.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: autogaita
-Version: 1.5.0
+Version: 1.5.1
 Summary: Automated Gait (and more!) Analysis in Python
 Author-email: Mahan Hosseini <autogaita@fz-juelich.de>
 License: GPLv3

autogaita-1.5.1/autogaita/batchrun_scripts/dlc_multirun.py

@@ -0,0 +1,73 @@
+from autogaita.common2D.common2D_utils import extract_info, run_singlerun_in_multirun
+
+# %% main function
+
+
+def dlc_multirun():
+    """
+    Batchrun script to run AutoGaitA DLC for a folder of datasets.
+    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 DLC GUI)
+    """
+    # folderinfo
+    folderinfo = {}
+    folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/"
+    folderinfo["sctable_filename"] = "25mm.xlsx"
+    folderinfo["data_string"] = "SIMINewOct"
+    folderinfo["beam_string"] = "BeamTraining"
+    folderinfo["premouse_string"] = "Mouse"
+    folderinfo["postmouse_string"] = "25mm"
+    folderinfo["prerun_string"] = "run"
+    folderinfo["postrun_string"] = "6DLC"
+    # cfg
+    cfg = {}
+    cfg["sampling_rate"] = 100  # base cfg
+    cfg["subtract_beam"] = True
+    cfg["dont_show_plots"] = False
+    cfg["convert_to_mm"] = True
+    cfg["pixel_to_mm_ratio"] = 3.76
+    cfg["x_sc_broken_threshold"] = 200  # optional cfg
+    cfg["y_sc_broken_threshold"] = 50
+    cfg["x_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["save_to_xls"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_y_at_SC_level"] = True
+    cfg["standardise_y_to_a_joint"] = True
+    cfg["y_standardisation_joint"] = ["Hind paw tao"]
+    cfg["plot_joint_number"] = 3
+    cfg["color_palette"] = "viridis"
+    cfg["legend_outside"] = True
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_x"] = True
+    cfg["standardise_x_coordinates"] = True
+    cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = ""
+    cfg["results_dir"] = ""
+    cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
+    cfg["fore_joints"] = [
+        "Front paw tao ",
+        "Wrist ",
+        "Elbow ",
+        "Lower Shoulder ",
+        "Upper Shoulder ",
+    ]
+    cfg["beam_col_left"] = ["BeamLeft"]  # list of len == 1
+    cfg["beam_col_right"] = ["BeamRight"]
+    cfg["beam_hind_jointadd"] = ["Tail base ", "Tail center ", "Tail tip "]
+    cfg["beam_fore_jointadd"] = ["Nose ", "Ear base "]
+    cfg["angles"] = {
+        "name": ["Ankle ", "Knee ", "Hip "],
+        "lower_joint": ["Hind paw tao ", "Ankle ", "Knee "],
+        "upper_joint": ["Knee ", "Hip ", "Iliac Crest "],
+    }
+    # run a single gaita run for each entry of info
+    info = extract_info("DLC", folderinfo)
+    for idx in range(len(info["name"])):
+        run_singlerun_in_multirun("DLC", idx, info, folderinfo, cfg)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    dlc_multirun()

autogaita-1.5.1/autogaita/batchrun_scripts/dlc_singlerun.py

@@ -0,0 +1,84 @@
+from autogaita.resources.utils import try_to_run_gaita
+import os
+
+
+# %% main function
+def dlc_singlerun():
+    """
+    Batchrun script to run AutoGaitA DLC for a single dataset.
+    folderinfo & cfg dictionaries must be configured as explained in our documentation. (note that each value of these corresponds to some object in the AutoGaitA DLC GUI)
+    """
+    # folderinfo
+    folderinfo = {}
+    folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/"
+    folderinfo["sctable_filename"] = "25mm.xlsx"
+    folderinfo["results_dir"] = ""
+    folderinfo["data_string"] = "SIMINewOct"
+    folderinfo["beam_string"] = "BeamTraining"
+    folderinfo["premouse_string"] = "Mouse"
+    folderinfo["postmouse_string"] = "25mm"
+    folderinfo["prerun_string"] = "run"
+    folderinfo["postrun_string"] = "6DLC"
+    # cfg
+    cfg = {}
+    cfg["sampling_rate"] = 100  # base cfg
+    cfg["subtract_beam"] = True
+    cfg["dont_show_plots"] = True
+    cfg["convert_to_mm"] = True
+    cfg["pixel_to_mm_ratio"] = 3.76
+    cfg["x_sc_broken_threshold"] = 200  # optional cfg
+    cfg["y_sc_broken_threshold"] = 50
+    cfg["x_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["save_to_xls"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_y_at_SC_level"] = False
+    cfg["standardise_y_to_a_joint"] = True
+    cfg["y_standardisation_joint"] = ["Hind paw tao"]
+    cfg["plot_joint_number"] = 5
+    cfg["color_palette"] = "Set2"
+    cfg["legend_outside"] = True
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_x"] = True
+    cfg["standardise_x_coordinates"] = True
+    cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = (
+        "/Users/mahan/sciebo/PythonCode/gaita_repo/autogaita/resources/Coordinate Standardisation Table Template.xlsx"
+    )
+    cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
+    cfg["fore_joints"] = [
+        "Front paw tao ",
+        "Wrist ",
+        "Elbow ",
+        "Lower Shoulder ",
+        "Upper Shoulder ",
+    ]
+    cfg["beam_col_left"] = ["BeamLeft"]  # list of len == 1
+    cfg["beam_col_right"] = ["BeamRight"]
+    cfg["beam_hind_jointadd"] = ["Tail base ", "Tail center ", "Tail tip "]
+    cfg["beam_fore_jointadd"] = ["Nose ", "Ear base "]
+    cfg["angles"] = {
+        "name": ["Ankle ", "Knee ", "Hip "],
+        "lower_joint": ["Hind paw tao ", "Ankle ", "Knee "],
+        "upper_joint": ["Knee ", "Hip ", "Iliac Crest "],
+    }
+    # info
+    info = {}
+    info["mouse_num"] = 17
+    info["run_num"] = 3
+    info["name"] = "ID " + str(info["mouse_num"]) + " - Run " + str(info["run_num"])
+    if folderinfo["results_dir"]:
+        info["results_dir"] = os.path.join(folderinfo["results_dir"], info["name"])
+    else:
+        info["results_dir"] = os.path.join(
+            folderinfo["root_dir"], "Results", info["name"]
+        )
+    # run
+    try_to_run_gaita("DLC", info, folderinfo, cfg, False)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    dlc_singlerun()

autogaita-1.5.1/autogaita/batchrun_scripts/group_dlcrun.py

@@ -0,0 +1,108 @@
+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",
+        # Testing Dataset
+        # "one",
+        # "two",
+        # 6 Group Dataset
+        # "36w_5mm",
+        # "36w_12mm",
+        # "36w_25mm",
+        # "104w_5mm",
+        # "104w_12mm",
+        # "104w_25mm",
+    ]
+    folderinfo["group_dirs"] = [
+        # --------------------------
+        # 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/",
+        # --------------------------
+        # 6 Group Dataset (nothing needed)
+    ]
+    folderinfo["results_dir"] = (
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/GroupResults/"
+        # "/Users/mahan/Desktop/Test6GroupResults/"
+    )
+    folderinfo["load_dir"] = (
+        ""
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Final Mouse Results/AdultElder3BeamsForPaper"  # for 6 group analysis example
+    )
+    # cfg
+    cfg = {}
+    cfg["do_permtest"] = True
+    cfg["do_anova"] = True
+    cfg["anova_design"] = "RM ANOVA"
+    cfg["permutation_number"] = 100
+    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"] = ""
+    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["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-1.5.1/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -0,0 +1,70 @@
+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 = {}
+    for cfg["which_leg"] in ["left", "right"]:
+        # 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"] = ["Young", "Old"]
+        folderinfo["group_dirs"] = [
+            "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2/Young/",
+            "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2/Old/",
+        ]
+        folderinfo["results_dir"] = (
+            "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2/Group/"
+            + cfg["which_leg"]
+            + " leg/"
+        )
+        folderinfo["load_dir"] = ""
+        # cfg
+        cfg["do_permtest"] = True
+        cfg["do_anova"] = True
+        cfg["permutation_number"] = 10000
+        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
+        cfg["color_palette"] = "viridis"
+        cfg["legend_outside"] = True
+        cfg["dont_show_plots"] = True
+        cfg["anova_design"] = "Mixed ANOVA"
+        cfg["PCA_variables"] = [
+            # "Midfoot, " + cfg["which_leg"] + " Z",
+            # "Ankle, " + cfg["which_leg"] + " Z",
+            # "Knee, " + cfg["which_leg"] + " Z",
+            # "Hip, " + cfg["which_leg"] + " Z",
+            # "Skullbase Angle",
+            # "Elbow, " + cfg["which_leg"] + " Angle",
+            # "Pelvis Z",
+            # "Shoulder, " + cfg["which_leg"] + " Z",
+        ]
+        cfg["stats_variables"] = [
+            "Ankle, " + cfg["which_leg"] + " Z",
+            "Ankle, " + cfg["which_leg"] + " Y",
+            "Ankle, " + cfg["which_leg"] + " Velocity",
+            "Ankle, " + cfg["which_leg"] + " Acceleration",
+            "Ankle, " + cfg["which_leg"] + " Angle",
+            "Ankle, " + cfg["which_leg"] + " Angle Velocity",
+            "Ankle, " + cfg["which_leg"] + " Angle Acceleration",
+            # "Knee, " + cfg["which_leg"] + " Z",
+            # "Shoulder, " + cfg["which_leg"] + " Angle",
+            # "Skullbase Angle",
+            # "Elbow, " + cfg["which_leg"] + " Angle",
+        ]
+        # run
+        autogaita.group(folderinfo, cfg)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    group_universal3Drun()

autogaita-1.5.1/autogaita/batchrun_scripts/sleap_singlerun.py

@@ -0,0 +1,82 @@
+from autogaita.resources.utils import try_to_run_gaita
+import os
+
+
+# main function
+def sleap_singlerun():
+    """
+    Batchrun script to run AutoGaitA SLEAP for a single dataset.
+    folderinfo & cfg dictionaries must be configured as explained in our documentation. (note that each value of these corresponds to some object in the AutoGaitA Simi GUI)
+    """
+    # folderinfo
+    folderinfo = {}
+    folderinfo["root_dir"] = (
+        "/Users/mahan/sciebo/Research/AutoGaitA/SLEAP/Human/Analysis/Old/"
+    )
+    folderinfo["results_dir"] = ""
+    folderinfo["sctable_filename"] = "AnnotationTableOldSLEAP"
+    folderinfo["data_string"] = ""
+    folderinfo["beam_string"] = ""
+    folderinfo["premouse_string"] = "Human"
+    folderinfo["postmouse_string"] = "_Run"
+    folderinfo["prerun_string"] = "Run"
+    folderinfo["postrun_string"] = "_SLEAP"
+
+    # cfg
+    cfg = {}
+    # 25 Hz sampling rate for SLEAP's example fly dataset (3000 frames @ 2 minutes)
+    # https://github.com/talmolab/sleap/tree/main/docs/notebooks/analysis_example
+    cfg["sampling_rate"] = 100
+    cfg["subtract_beam"] = False
+    cfg["dont_show_plots"] = True
+    cfg["convert_to_mm"] = False
+    cfg["pixel_to_mm_ratio"] = 1
+    cfg["x_sc_broken_threshold"] = 200  # optional cfg
+    cfg["y_sc_broken_threshold"] = 50
+    cfg["x_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["save_to_xls"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_y_at_SC_level"] = False
+    cfg["standardise_y_to_a_joint"] = False
+    cfg["y_standardisation_joint"] = ["Midfoot"]
+    cfg["plot_joint_number"] = 7
+    cfg["color_palette"] = "viridis"
+    cfg["legend_outside"] = True
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_x"] = False
+    cfg["standardise_x_coordinates"] = False
+    cfg["x_standardisation_joint"] = ["Midfoot"]
+    cfg["coordinate_standardisation_xls"] = ""
+    cfg["hind_joints"] = ["Midfoot", "Ankle", "Knee", "Hip"]
+    cfg["fore_joints"] = []
+    cfg["beam_col_left"] = []  # list of len == 1
+    cfg["beam_col_right"] = []
+    cfg["beam_hind_jointadd"] = []
+    cfg["beam_fore_jointadd"] = []
+    cfg["angles"] = {
+        "name": ["Ankle", "Knee"],
+        "lower_joint": ["Midfoot", "Ankle"],
+        "upper_joint": ["Knee", "Hip"],
+    }
+
+    # info
+    info = {}
+    info["mouse_num"] = 32
+    info["run_num"] = 1
+    info["name"] = "ID " + str(info["mouse_num"]) + " - Run " + str(info["run_num"])
+    if folderinfo["results_dir"]:
+        info["results_dir"] = os.path.join(folderinfo["results_dir"], info["name"])
+    else:
+        info["results_dir"] = os.path.join(
+            folderinfo["root_dir"], "Results", info["name"]
+        )
+    # run
+    try_to_run_gaita("SLEAP", info, folderinfo, cfg, False)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    sleap_singlerun()

autogaita-1.5.1/autogaita/batchrun_scripts/universal3D_multirun.py

@@ -0,0 +1,112 @@
+from autogaita.resources.utils import try_to_run_gaita
+import os
+import copy
+
+# %% main function
+
+
+def universal3D_multirun():
+    """
+    Batchrun script to run AutoGaitA Universal 3D for a folder of datasets.
+    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 Universal 3D GUI)
+    """
+    # folderinfo
+    folderinfo = {}
+    folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2/"
+    folderinfo["results_dir"] = ""
+    folderinfo["sctable_filename"] = "SC Latency Table"
+    folderinfo["postname_string"] = ""
+    # cfg
+    cfg = {}
+    cfg["sampling_rate"] = 100  # base cfg
+    cfg["dont_show_plots"] = True
+    cfg["y_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = 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["coordinate_standardisation_xls"] = ""
+    cfg["joints"] = ["Midfoot", "Ankle", "Knee", "Hip", "Pelvis", "Shoulder", "Neck"]
+    cfg["angles"] = {
+        "name": ["Ankle", "Knee"],
+        "lower_joint": ["Midfoot", "Ankle"],
+        "upper_joint": ["Knee", "Hip"],
+    }
+    # run a single gaita run for each entry of info
+    info = extract_info(folderinfo)
+    for idx, name in enumerate(info["name"]):
+        run_singlerun(idx, info, folderinfo, cfg)
+
+
+# %% local functions
+
+
+def run_singlerun(idx, info, folderinfo, cfg):
+    """Run the main code of individual run-analyses based on current cfg"""
+    # extract and pass info of this mouse/run (also update resdir)
+    this_info = {}
+    keynames = info.keys()
+    for keyname in keynames:
+        this_info[keyname] = info[keyname][idx]
+    # make a deep copy of cfg that used in each run, otherwise changes to the cfg dict
+    # would translate to subsequent runs
+    # ==> see https://stackoverflow.com/questions/2465921/
+    #         how-to-copy-a-dictionary-and-only-edit-the-copy
+    this_cfg = copy.deepcopy(cfg)
+    # important to only pass this_info to main script here (1 run at a time!)
+    try_to_run_gaita("Universal 3D", this_info, folderinfo, this_cfg, True)
+
+
+def extract_info(folderinfo):
+    """Prepare a dict of lists that include unique name infos"""
+    root_dir = folderinfo["root_dir"]
+    results_dir = folderinfo["results_dir"]
+    sctable_filename = folderinfo["sctable_filename"]
+    postname_string = folderinfo["postname_string"]
+    info = {"name": [], "results_dir": []}
+    for filename in os.listdir(root_dir):
+        # dont try to combine the two "join" if blocks into one - we want to append
+        # results dir WHENEVER we append name!
+        if not postname_string:
+            # dont use endswith below to catch .xlsx too
+            if (".xls" in filename) & (sctable_filename not in filename):
+                info["name"].append(filename.split(".xls")[0])
+                if results_dir:
+                    info["results_dir"].append(
+                        os.path.join(results_dir, info["name"][-1])
+                    )
+                else:
+                    info["results_dir"].append(
+                        os.path.join(root_dir, "Results", info["name"][-1])
+                    )
+        else:
+            if postname_string in filename:
+                info["name"].append(filename.split(postname_string)[0])
+                if results_dir:
+                    info["results_dir"].append(
+                        os.path.join(results_dir, info["name"][-1])
+                    )
+                else:
+                    info["results_dir"].append(
+                        os.path.join(root_dir, "Results", info["name"][-1])
+                    )
+    if len(info["name"]) < 1:
+        no_files_message = (
+            f"Unable to find any files at {root_dir}!" + "\ncheck your inputs!"
+        )
+        print(no_files_message)
+    return info
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    universal3D_multirun()

autogaita-1.5.1/autogaita/batchrun_scripts/universal3D_singlerun.py

@@ -0,0 +1,67 @@
+from autogaita.resources.utils import try_to_run_gaita
+import os
+
+
+# main function
+def universal3D_singlerun():
+    """
+    Batchrun script to run AutoGaitA Universal 3D for a single dataset.
+    folderinfo & cfg dictionaries must be configured as explained in our documentation. (note that each value of these corresponds to some object in the AutoGaitA Universal 3D GUI)
+    """
+    # folderinfo
+    folderinfo = {}
+    folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2/"
+    # folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Fly/3D Data/"
+    folderinfo["results_dir"] = ""
+    folderinfo["sctable_filename"] = "SC Latency Table"
+    folderinfo["postname_string"] = ""
+    # cfg
+    cfg = {}
+    cfg["sampling_rate"] = 100  # base cfg
+    cfg["dont_show_plots"] = True
+    cfg["y_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_z_at_SC_level"] = True
+    cfg["standardise_z_to_a_joint"] = True
+    cfg["z_standardisation_joint"] = ["Midfoot, left"]
+    cfg["plot_joint_number"] = 5
+    cfg["color_palette"] = "Set2"
+    cfg["legend_outside"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_y"] = True
+    cfg["standardise_y_coordinates"] = True
+    cfg["y_standardisation_joint"] = ["Midfoot, left"]
+    cfg["coordinate_standardisation_xls"] = ""
+    cfg["joints"] = [
+        # "R1-ThCx",
+        "Midfoot",
+        "Ankle",
+        "Knee",
+        "Hip",
+        "Pelvis",
+        "Shoulder",
+        "Neck",
+    ]
+    cfg["angles"] = {
+        "name": ["Ankle", "Knee"],
+        "lower_joint": ["Midfoot", "Ankle"],
+        "upper_joint": ["Knee", "Hip"],
+    }
+    # info
+    info = {}
+    info["name"] = "SK"  # "A1"  #  # analyse this dataset
+    if folderinfo["results_dir"]:
+        info["results_dir"] = os.path.join(folderinfo["results_dir"], info["name"])
+    else:
+        info["results_dir"] = os.path.join(
+            folderinfo["root_dir"], "Results", info["name"]
+        )
+    # run
+    try_to_run_gaita("Universal 3D", info, folderinfo, cfg, False)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    universal3D_singlerun()