autogaita 1.0.8__tar.gz → 1.0.9__tar.gz

{autogaita-1.0.8 → autogaita-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.8
+Version: 1.0.9
 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-1.0.8 → autogaita-1.0.9}/README.md

@@ -81,6 +81,9 @@ Step cycles are normalised via averaging temporally adjacent data points if thei
 
 **We strongly advise** users to think carefully about an appropriate bin number for their datasets. The correct value varies and depends strongly on the studied species, behaviour and the frame rate of cameras.
 
+## 2D Kinematics in AutoGaitA Universal 3D
+**We strongly advise** AutoGaitA Universal 3D users to carefully consider how our toolbox computes kinematics in 2D, i.e., angles along the y/z-plane and velocities along the y-dimensions. For more information, please see the corresponding **[important note on 2D kinematics in our documentation](https://docs.google.com/document/d/1iQxSwqBW3VdIXHm-AtV4TGlgpJPDldogVx6qzscsGxA/edit?tab=t.0#heading=h.xc5ome7hzfid)**.
+
 ## Analysing other behaviours - AutoCyclA 🚴
 Even though AutoGaitA's main focus is to automate and standardise gait analyses, our toolbox can be used to automate the analyses of any rhythmic behaviour of interest. For a proof-of-principle demonstration and an introduction of the general workflow of such analyses, see **[AutoCyclA - Automated Cycling Analysis with AutoGaitA.](https://github.com/mahan-hosseini/AutoGaitA/tree/main/autocycla)**
 

{autogaita-1.0.8 → autogaita-1.0.9}/autogaita/__init__.py

@@ -1,7 +1,7 @@
 # main gui
 from .gui.main_gui import run_gui  # autogaita.run_gui()
 
-# 3 sub-guis
+# 4 sub-guis
 from .gui.dlc_gui import run_dlc_gui  # autogaita.run_dlc_gui()
 from .gui.sleap_gui import run_sleap_gui  # autogaita.run_sleap_gui()
 from .gui.universal3D_gui import (
@@ -17,7 +17,7 @@ from .universal3D.universal3D_main import (
 )  # autogaita.universal3D(info, folderinfo, cfg)
 from .group.group_main import group  # autogaita.group(folderinfo, cfg)
 
-# 6 batchrun functions - call via e.g. autogaita.dlc_singlerun()
+# 7 batchrun functions - call via e.g. autogaita.dlc_singlerun()
 from .batchrun_scripts.dlc_singlerun import dlc_singlerun
 from .batchrun_scripts.dlc_multirun import dlc_multirun
 from .batchrun_scripts.sleap_singlerun import sleap_singlerun

{autogaita-1.0.8 → autogaita-1.0.9}/autogaita/batchrun_scripts/dlc_multirun.py

@@ -1,5 +1,4 @@
 from autogaita.common2D.common2D_utils import extract_info, run_singlerun_in_multirun
-import os
 
 # %% main function
 
@@ -63,7 +62,7 @@ def dlc_multirun():
         "upper_joint": ["Knee ", "Hip ", "Iliac Crest "],
     }
     # run a single gaita run for each entry of info
-    info = extract_info(folderinfo)
+    info = extract_info("DLC", folderinfo)
     for idx in range(len(info["name"])):
         run_singlerun_in_multirun("DLC", idx, info, folderinfo, cfg)
 

autogaita-1.0.9/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-1.0.8 → autogaita-1.0.9}/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -27,8 +27,10 @@ def group_universal3Drun():
         # cfg
         cfg["do_permtest"] = True
         cfg["do_anova"] = True
-        cfg["permutation_number"] = 10
+        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

{autogaita-1.0.8 → autogaita-1.0.9}/autogaita/batchrun_scripts/sleap_singlerun.py

@@ -11,18 +11,22 @@ def sleap_singlerun():
     # folderinfo
     folderinfo = {}
     folderinfo["root_dir"] = (
-        "/Users/mahan/sciebo/Research/AutoGaitA/SLEAP/SLEAPs Drosophila/"
+        "/Users/mahan/sciebo/Research/AutoGaitA/SLEAP/Human/Analysis/Old/"
     )
     folderinfo["results_dir"] = ""
-    folderinfo["sctable_filename"] = "Annotation Table"
-    folderinfo["data_string"] = "_data"
+    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"] = 25
+    cfg["sampling_rate"] = 100
     cfg["subtract_beam"] = False
     cfg["dont_show_plots"] = True
     cfg["convert_to_mm"] = False
@@ -35,31 +39,33 @@ def sleap_singlerun():
     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"] = ["head"]
-    cfg["plot_joint_number"] = 3
+    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"] = False
-    cfg["flip_gait_direction"] = False
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
     cfg["analyse_average_x"] = False
     cfg["standardise_x_coordinates"] = False
-    cfg["x_standardisation_joint"] = ["head"]
-    cfg["hind_joints"] = ["head", "thorax", "wingL", "wingR"]
+    cfg["x_standardisation_joint"] = ["Midfoot"]
+    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": ["thorax"],
-        "lower_joint": ["hindlegL4"],
-        "upper_joint": ["midlegL4"],
+        "name": ["Ankle", "Knee"],
+        "lower_joint": ["Midfoot", "Ankle"],
+        "upper_joint": ["Knee", "Hip"],
     }
 
     # info
     info = {}
-    info["name"] = "1"  # analyse this dataset
+    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:

{autogaita-1.0.8 → autogaita-1.0.9}/autogaita/batchrun_scripts/universal3D_multirun.py

@@ -1,6 +1,6 @@
 from autogaita.resources.utils import try_to_run_gaita
 import os
-
+import copy
 
 # %% main function
 
@@ -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"],
@@ -51,8 +56,13 @@ def run_singlerun(idx, info, folderinfo, cfg):
     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, cfg, True)
+    try_to_run_gaita("Universal 3D", this_info, folderinfo, this_cfg, True)
 
 
 def extract_info(folderinfo):
@@ -88,6 +98,11 @@ def extract_info(folderinfo):
                     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
 
 

{autogaita-1.0.8 → autogaita-1.0.9}/autogaita/batchrun_scripts/universal3D_singlerun.py

@@ -18,16 +18,21 @@ def universal3D_singlerun():
     # cfg
     cfg = {}
     cfg["sampling_rate"] = 100  # base cfg
-    cfg["dont_show_plots"] = False
+    cfg["dont_show_plots"] = True
     cfg["y_acceleration"] = True
     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, left"]
     cfg["plot_joint_number"] = 5
     cfg["color_palette"] = "Set2"
     cfg["legend_outside"] = True
-    cfg["analyse_average_y"] = False
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_y"] = True
+    cfg["standardise_y_coordinates"] = True
+    cfg["y_standardisation_joint"] = ["Midfoot, left"]
     cfg["joints"] = [
         # "R1-ThCx",
         "Midfoot",