autogaita 0.4.0__tar.gz → 0.4.1__tar.gz

{autogaita-0.4.0 → autogaita-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 0.4.0
+Version: 0.4.1
 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-0.4.0 → autogaita-0.4.1}/README.md

@@ -20,7 +20,7 @@
 
 It is strongly recommended that a separate virtual environment for AutoGaitA is created (note that the approach below creates the virtual environment to your current directory):
 
-- Create the virtual environment
+- Create the virtual environment:
     - `python -m venv env_gaita`
 
 - After creation, activate the virtual environment via:
@@ -29,17 +29,22 @@ It is strongly recommended that a separate virtual environment for AutoGaitA is
 
 - Once activated, install AutoGaitA in the virtual environment via pip: `pip install autogaita`.
 
-- Access the main user interface via `python -m autogaita`.
+- Access the main user interface via: `python -m autogaita`.
 
 - To update to the latest release (see the *Releases* panel on the right for the latest release) activate the virtual environment and: `pip install autogaita -U`. 
 
-## Tutorials and Examples
+## Demo Video
+*Check out the video below for a demonstration of AutoGaitA's main workflow!*
+<p><a href="https://youtu.be/_HIZVuUzpzk?feature=shared">
+<img src="https://github.com/mahan-hosseini/AutoGaitA/blob/main/res/pic_to_demo_for_repo.png" width="550">
 
-### Video Walkthrough Tutorials
+## Tutorials & Examples
 
-**[The AutoGaitA YouTube Channel](https://youtube.com/playlist?list=PLCn5T7K_H8K56NIcEsfDK664OP7cN_Bad&si=mV5p2--nYvbofkPh) provides tutorials for file preparation and instructions on how to use AutoGaitA**
+### Walkthrough Tutorial Videos  
 
-*Please note that tutorial videos might not always reflect the most up-to-date version of our toolbox, especially in the beginning when things are regularly changing. We will make sure to record new videos whenever there are major changes, though.*
+**[The AutoGaitA YouTube Channel](https://youtube.com/playlist?list=PLCn5T7K_H8K56NIcEsfDK664OP7cN_Bad&si=mV5p2--nYvbofkPh) provides tutorials for file preparation and instructions on how to use AutoGaitA. This includes in-depth explanations of all details, (main & advanced) configurations, possibilities, and outputs.**
+
+*Please note that tutorial videos might not always reflect the most up-to-date version of our toolbox, especially in the beginning when things are regularly changing. We will make sure to record new videos whenever there are major changes though. Last tutorial-update was with v0.4.0. (August 2024).*
 
 ### Example Data
 We provide an example dataset in the **example data** folder of this repository, with a set of mice walking over differently wide beams and both the beam as well as body coordinates being tracked with DLC. Note that this dataset was used in our tutorial videos introducing *AutoGaitA_DLC*, *AutoGaitA_Group* and in our video explaining file preparation for *AutoGaitA_DLC*.  We further provide a **group** folder there that can be used alongside the *AutoGaitA_Group* tutorial to confirm that users generate the same set of results following our instructions.
@@ -47,7 +52,7 @@ We provide an example dataset in the **example data** folder of this repository,
 ### Annotation Table Examples and Templates
 Annotation Table example and template files for *AutoGaitA_DLC* and *AutoGaitA_Simi* can be found in the [**annotation tables**](https://github.com/mahan-hosseini/AutoGaitA/tree/main/annotation%20tables) folder of this repository.
 
-Users are advised to read the ***important note*** of that folder, use the template to enter their data's timestamp information and to then compare the resulting table with our example to check formatting. Users working with ImageJ/FIJI are encouraged to check out the [AnnotationTable-Plugin](https://github.com/luca-flemming/AnnotationTable-Plugin) developed by our contributor Luca Flemming.
+Users are advised to read the **General Recommendations** section of that folder, use the template to enter their data's timestamp information and to then compare the resulting table with our example to check formatting. Users working with ImageJ/FIJI are encouraged to check out the [AnnotationTable-Plugin](https://github.com/luca-flemming/AnnotationTable-Plugin) developed by our contributor Luca Flemming.
 
 ## Documentation
 
@@ -59,8 +64,8 @@ Users are advised to read the ***important note*** of that folder, use the templ
 By default, *AutoGaitA DLC* and *AutoGaitA Simi* implement standard values for mouse and human locomotion, respectively. If your analysis deviates from these standards (e.g. by focussing on another limb or a different species) **you must change these values!** You can find the window in the *advanced configuration* sections and once values are customised they remain for subsequent executions of AutoGaitA (i.e., until the program is closed). 
 
 **Find out more about *AutoGaitA's custom joints and angles:***
-- [YouTube - AutoGaitA DLC Advanced Configuration](https://youtu.be/YABoQMOqChk?feature=shared) 
-- [YouTube - AutoGaitA Simi](https://youtu.be/fJhnjrJbA5c?feature=shared) 
+- [YouTube - AutoGaitA DLC Advanced Configuration](https://youtu.be/MP9g9kXRE_Q?feature=shared) 
+- [YouTube - AutoGaitA Simi](https://youtu.be/rTG-Fc9XI9g?feature=shared) 
 - [Documentation - AutoGaitA DLC](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.20bg7b7ymt0b)
 - [Documentation - AutoGaitA Simi](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.uz61bpmua7qz)
 

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/autogaita_dlc.py

@@ -1286,10 +1286,13 @@ def standardise_x_y_and_add_features_to_one_step(step, cfg):
         else:
             this_y_min = step_copy[y_cols].min().min()
         step_copy[y_cols] -= this_y_min
-    # add angles and velocities
-    step_copy = add_features(step_copy, cfg)
-    # standardise x (horizontal dimension) at step-cycle level too
-    if cfg["standardise_x_coordinates"] is True:
+    # 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
+        # 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")]
         # note the [0] here is important because it's still a list of len=1!!
@@ -1298,9 +1301,7 @@ def standardise_x_y_and_add_features_to_one_step(step, cfg):
         ].min()
         x_norm_step[x_cols] -= min_x_standardisation_joint
         x_norm_step = add_features(x_norm_step, cfg)
-        return step_copy, x_norm_step
-    else:
-        return step_copy
+        return non_norm_step, x_norm_step
 
 
 def add_features(step, cfg):
@@ -1308,10 +1309,11 @@ def add_features(step, cfg):
     # unpack
     hind_joints = cfg["hind_joints"]
     angles = cfg["angles"]
+    if hind_joints:
+        step = add_x_velocities(step, cfg)
     if angles["name"]:  # if there is at least 1 string in the list
         step = add_angles(step, cfg)
-    if hind_joints:
-        step = add_velocities(step, cfg)
+        step = add_angular_velocities(step, cfg)
     return step
 
 
@@ -1356,28 +1358,31 @@ def compute_angle(joint_angle, joint2, joint3):
     return math.degrees(angle)
 
 
-def add_velocities(step, cfg):
-    """Feature #2: Joint x and Angular Velocities"""
+def add_x_velocities(step, cfg):
+    """Feature #2: Joint x Velocities & Accelerations"""
     # unpack
     hind_joints = cfg["hind_joints"]
     x_acceleration = cfg["x_acceleration"]
-    angular_acceleration = cfg["angular_acceleration"]
-    # compute velocities (& acceleration if wanted) for hind joints first
+
     for joint in hind_joints:
         step[joint + "Velocity"] = 0.0
         if x_acceleration:
             step[joint + "Acceleration"] = 0.0
-        # step[joint + "Accel. Gradient"] = 0.0
     for joint in hind_joints:
         step.loc[:, joint + "Velocity"] = np.gradient(step.loc[:, joint + "x"])
         if x_acceleration:
             step.loc[:, joint + "Acceleration"] = np.gradient(
                 step.loc[:, joint + "Velocity"]
             )
-        # step.loc[:, joint + "Accel. Gradient"]= np.gradient(
-        #     step.loc[:, joint + "Acceleration"])
-    # compute velocities (& acceleration) for the angles too
-    angle_cols = [c for c in step.columns if "Angle" in c]
+    return step
+
+
+def add_angular_velocities(step, cfg):
+    """Feature #3: Angular Velocities & Accelerations"""
+    # unpack
+    angular_acceleration = cfg["angular_acceleration"]
+
+    angle_cols = [c for c in step.columns if c.endswith("Angle")]
     for angle in angle_cols:
         step[angle + " Velocity"] = 0.0  # space is correct here
         if angular_acceleration:

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/autogaita_group_gui.py

@@ -82,7 +82,7 @@ COLOR_PALETTES_LIST = [
     "cividis_r",  # uniform palettes in reversed order
 ]
 EXCLUDED_VARS_FROM_CFG_FILE = ["last_runs_stats_variables", "last_runs_PCA_variables"]
-AV_SHEET_NAME = "Average Stepcycle"
+NORM_SHEET_NAME = "Normalised Stepcycle"
 WINDOWS_TASKBAR_MAXHEIGHT = 72
 
 # To get the path of the autogaita folder I use __file__
@@ -134,7 +134,7 @@ def group_gui():
     root_dimensions = (root_w, root_h, root_x, root_y)
     # set the dimensions of the screen and where it is placed
     root.geometry("%dx%d+%d+%d" % root_dimensions)
-    root.title("AutoGaitA Group")
+    root.title("Group GaitA")
 
     # nested function: main window
     def mainwindow(root, group_number, root_dimensions):
@@ -230,7 +230,7 @@ def build_mainwindow(root, group_number, root_dimensions):
         # ........................  geometry & intro section  ..........................
         # geometry
         mainwindow = ctk.CTkToplevel(root)
-        mainwindow.title("AutoGaitA Group")
+        mainwindow.title("Group GaitA")
         # set the dimensions of the screen and where it is placed
         # => have it half-wide starting at 1/4 of screen's width (dont change w & x!)
         mainwindow.geometry(
@@ -668,7 +668,7 @@ def definefeatures_window(
         # next operator means we loop lazy - stop once we find it & return None if av
         # sheet not in dir
         av_sheet_path = next(
-            (file for file in IDs_files if AV_SHEET_NAME in file), None
+            (file for file in IDs_files if NORM_SHEET_NAME in file), None
         )
         if av_sheet_path:  # won't be true if no AVXLS found
             full_path = os.path.join(some_IDs_dir, av_sheet_path)

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/autogaita_simi_gui.py

@@ -378,6 +378,7 @@ def build_cfg_window(root, cfg, root_dimensions):
     screen_height = root.winfo_screenheight()  # height of the screen
     # build window
     cfg_window = ctk.CTkToplevel(root)
+    cfg_window.title("Advanced Configuration")
     cfg_window.geometry(
         f"{int(screen_width/2)}x{screen_height}+{int(screen_width/4)}+0"
     )

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/batchrun_scripts/autogaita_dlc_singlerun.py

@@ -33,7 +33,7 @@ def dlc_singlerun():
     cfg["save_to_xls"] = True
     cfg["bin_num"] = 25
     cfg["plot_SE"] = True
-    cfg["standardise_y_at_SC_level"] = 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"] = 3

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/dlc_gui_config.json

@@ -1,22 +1,22 @@
 [
     {
-        "mouse_num": "",
-        "run_num": "",
-        "root_dir": "",
-        "sctable_filename": "",
-        "data_string": "",
-        "beam_string": "",
-        "premouse_string": "",
-        "postmouse_string": "",
-        "prerun_string": "",
-        "postrun_string": ""
+        "mouse_num": "14",
+        "run_num": "1",
+        "root_dir": "/Users/mahan/sciebo/Research/AutoGaitA/CRC Demo Files/CRC_Demo_Mice/",
+        "sctable_filename": "25mm",
+        "data_string": "SIMINewOct",
+        "beam_string": "BeamTrain",
+        "premouse_string": "Mouse",
+        "postmouse_string": "25mm",
+        "prerun_string": "run",
+        "postrun_string": "-6DLC"
     },
     {
-        "sampling_rate": "",
-        "subtract_beam": false,
+        "sampling_rate": "100",
+        "subtract_beam": true,
         "dont_show_plots": false,
-        "convert_to_mm": false,
-        "pixel_to_mm_ratio": "",
+        "convert_to_mm": true,
+        "pixel_to_mm_ratio": "3.76",
         "x_sc_broken_threshold": "200",
         "y_sc_broken_threshold": "50",
         "x_acceleration": true,
@@ -24,8 +24,8 @@
         "save_to_xls": true,
         "bin_num": "25",
         "plot_joint_number": "3",
-        "plot_SE": false,
-        "standardise_y_at_SC_level": false,
+        "plot_SE": true,
+        "standardise_y_at_SC_level": true,
         "standardise_y_to_a_joint": true,
         "y_standardisation_joint": [
             "Hind paw tao"
@@ -41,11 +41,9 @@
         "legend_outside": true,
         "results_dir": "",
         "hind_joints": [
-            "Hind paw tao ",
-            "Ankle ",
-            "Knee ",
-            "Hip ",
-            "Iliac Crest "
+            "Foot",
+            "Shoulder",
+            "Knee "
         ],
         "fore_joints": [
             "Front paw tao ",
@@ -73,17 +71,20 @@
             "name": [
                 "Ankle",
                 "Knee",
-                "Hip"
+                "Hip",
+                "Elbow"
             ],
             "lower_joint": [
                 "Hind paw tao",
                 "Ankle",
-                "Knee"
+                "Knee",
+                "Wrist"
             ],
             "upper_joint": [
                 "Knee",
                 "Hip",
-                "Iliac Crest"
+                "Iliac Crest",
+                "Shoulder"
             ]
         }
     }

autogaita-0.4.1/autogaita/group_gui_config.json

@@ -0,0 +1,69 @@
+[
+    {
+        "group_names": [
+            "5 mm",
+            "12 mm",
+            "25 mm ",
+            "",
+            "",
+            ""
+        ],
+        "group_dirs": [
+            "/Users/mahan/sciebo/PythonCode/autogaita_repository/example data/5mm/Results",
+            "/Users/mahan/sciebo/PythonCode/autogaita_repository/example data/12mm/Results",
+            "/Users/mahan/sciebo/PythonCode/autogaita_repository/example data/25mm/Results",
+            "",
+            "",
+            ""
+        ],
+        "results_dir": "/Users/mahan/Desktop/GroupResults/"
+    },
+    {
+        "do_permtest": false,
+        "do_anova": true,
+        "anova_design": "RM ANOVA",
+        "permutation_number": 10000,
+        "stats_threshold": "0.05",
+        "which_leg": "right",
+        "number_of_PCs": 3,
+        "save_3D_PCA_video": false,
+        "plot_SE": false,
+        "color_palette": "viridis",
+        "dont_show_plots": false,
+        "legend_outside": true,
+        "stats_variables": [
+            "Ankle y"
+        ],
+        "PCA_variables": [
+            "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 x",
+            "Tail base y",
+            "Tail center x",
+            "Tail center y",
+            "Tail tip x",
+            "Tail tip y",
+            "Ankle Angle",
+            "Knee Angle",
+            "Hip Angle",
+            "Hind paw tao Velocity",
+            "Hind paw tao Acceleration",
+            "Ankle Velocity"
+        ]
+    }
+]

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita/simi_gui_config.json

@@ -1,14 +1,14 @@
 [
     {
-        "name": "",
-        "root_dir": "",
-        "sctable_filename": "",
+        "name": "Control_1",
+        "root_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Human/Testing2",
+        "sctable_filename": "SC Latency Table",
         "postname_flag": false,
         "postname_string": ""
     },
     {
         "analyse_singlerun": false,
-        "sampling_rate": "",
+        "sampling_rate": "100",
         "dont_show_plots": false,
         "y_acceleration": true,
         "angular_acceleration": true,
@@ -16,8 +16,8 @@
         "plot_joint_number": "3",
         "plot_SE": false,
         "normalise_height_at_SC_level": true,
-        "analyse_average_y": false,
-        "color_palette": "viridis",
+        "analyse_average_y": true,
+        "color_palette": "Set2",
         "legend_outside": true,
         "results_dir": "",
         "joints": [
@@ -25,23 +25,31 @@
             "Ankle ",
             "Knee ",
             "Hip ",
-            "Pelvis "
+            "Pelvis ",
+            "",
+            ""
         ],
         "angles": {
             "name": [
                 "Ankle",
                 "Knee",
-                "Hip"
+                "Hip",
+                "",
+                ""
             ],
             "lower_joint": [
                 "Midfoot",
                 "Ankle",
-                "Knee"
+                "Knee",
+                "",
+                ""
             ],
             "upper_joint": [
                 "Knee",
                 "Hip",
-                "Pelvis"
+                "Pelvis",
+                "",
+                ""
             ]
         }
     }

{autogaita-0.4.0 → autogaita-0.4.1}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 0.4.0
+Version: 0.4.1
 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-0.4.0 → autogaita-0.4.1}/setup.py

@@ -25,7 +25,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="0.4.0",  # rc == release candidate (before release is finished)
+    version="0.4.1",  # 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=["autogaita", "autogaita.batchrun_scripts"],

{autogaita-0.4.0 → autogaita-0.4.1}/tests/test_dlc_unit3_main_analysis.py

@@ -3,7 +3,7 @@ from autogaita.autogaita_dlc import (
     extract_stepcycles,
     analyse_and_export_stepcycles,
 )
-from autogaita.autogaita_dlc import add_angles, add_velocities
+from autogaita.autogaita_dlc import add_angles, add_x_velocities, add_angular_velocities
 from autogaita.autogaita_dlc import standardise_x_y_and_add_features_to_one_step
 from hypothesis import given
 import hypothesis.strategies as st
@@ -217,7 +217,8 @@ def test_velocities():
         "x_acceleration": True,
         "angular_acceleration": True,
     }
-    step = add_velocities(step, cfg)
+    step = add_x_velocities(step, cfg)
+    step = add_angular_velocities(step, cfg)
     # expected values were obtained by calling np.gradient on arrays above
     expected_values = {
         "Sample Velocity": [2.0, 2.0, 3.0, 2.0, -2.0, -3.0, -2.0, -2.0, -5.0, -8.0],

autogaita-0.4.0/autogaita/group_gui_config.json

@@ -1,37 +0,0 @@
-[
-    {
-        "group_names": [
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
-        ],
-        "group_dirs": [
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
-        ],
-        "results_dir": ""
-    },
-    {
-        "do_permtest": true,
-        "do_anova": false,
-        "anova_design": "",
-        "permutation_number": "10000",
-        "stats_threshold": "0.05",
-        "which_leg": "right",
-        "number_of_PCs": 3,
-        "save_3D_PCA_video": false,
-        "plot_SE": false,
-        "color_palette": "viridis",
-        "dont_show_plots": false,
-        "legend_outside": true,
-        "stats_variables": [],
-        "PCA_variables": []
-    }
-]