autogaita 0.0.6__tar.gz → 0.1.0__tar.gz

autogaita-0.1.0/PKG-INFO

@@ -0,0 +1,23 @@
+Metadata-Version: 2.1
+Name: autogaita
+Version: 0.1.0
+Summary: Automatic Gait Analysis in Python
+Home-page: https://github.com/mahan-hosseini/AutoGaitA/
+Author: Mahan Hosseini
+License: GPLv3
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: customtkinter>=5.2
+Requires-Dist: pandas>=2.0
+Requires-Dist: numpy>=1.24
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: pingouin>=0.5
+Requires-Dist: scipy>=1.11
+Requires-Dist: ffmpeg-python>=0.2
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pillow>=10.3
+Requires-Dist: pyobjc
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: hypothesis; extra == "dev"

{autogaita-0.0.6 → autogaita-0.1.0}/README.md

@@ -1,8 +1,11 @@
 ![AutoGaitA](https://github.com/mahan-hosseini/AutoGaitA/blob/main/res/autogaita_logo.png?raw=true)
-[![PyPI version](https://badge.fury.io/py/autogaita.svg)](https://badge.fury.io/py/autogaita)
+![Repository Active](https://www.repostatus.org/badges/latest/active.svg)
 [![Test AutoGaitA](https://github.com/mahan-hosseini/AutoGaitA/actions/workflows/auto_test_gaita.yml/badge.svg)](https://github.com/mahan-hosseini/AutoGaitA/actions/workflows/auto_test_gaita.yml)
 ![Python](https://img.shields.io/badge/python-v3.10+-blue.svg)
-![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/autogaita)](https://pypi.org/project/autogaita/)
+![license: GPL v3](https://img.shields.io/badge/license-GPLv3-blue.svg)
+[![paper: biorxiv](https://img.shields.io/badge/paper-biorxiv-blue)](https://doi.org/10.1101/2024.04.14.589409) 
+
 ![Black](https://img.shields.io/badge/code%20style-black-000000.svg)
 # Automated Gait Analysis in Python 🐸
 
@@ -34,6 +37,8 @@ It is strongly recommended that a separate virtual environment for AutoGaitA is
 
 **[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**
 
+*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.*
+
 ### 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.
 

{autogaita-0.0.6 → autogaita-0.1.0}/autogaita/autogaita.py

@@ -6,7 +6,6 @@ from PIL import Image, ImageTk
 from importlib import resources
 import platform
 
-
 # %% global constants
 TXT_COLOR = "#ffffff"  # white
 FONT_SIZE = 20

{autogaita-0.0.6 → autogaita-0.1.0}/autogaita/autogaita_dlc.py

@@ -60,7 +60,7 @@ def dlc(info, folderinfo, cfg):
 
     # .........................  step-cycle extraction  ................................
     all_cycles = extract_stepcycles(data, info, folderinfo, cfg)
-    if all_cycles == None:
+    if not all_cycles:
         handle_issues("scs_invalid", info)
         return
 
@@ -71,7 +71,7 @@ def dlc(info, folderinfo, cfg):
     plot_results(info, results, folderinfo, cfg)
 
     # ............................  print finish  ......................................
-    print_finish(cfg)
+    print_finish(info, cfg)
 
 
 # %% local functions 1 - preparation
@@ -225,6 +225,7 @@ def some_prep(info, folderinfo, cfg):
     beam_hind_jointadd = cfg["beam_hind_jointadd"]
     beam_fore_jointadd = cfg["beam_fore_jointadd"]
     direction_joint = cfg["direction_joint"]
+    export_average_x = cfg["export_average_x"]
     # store config json file @ group path
     # !!! NU - do this @ mouse path!
     group_path = results_dir.split(name)[0]
@@ -233,6 +234,7 @@ def some_prep(info, folderinfo, cfg):
         "sampling_rate": sampling_rate,
         "convert_to_mm": convert_to_mm,
         "normalise_height_at_SC_level": normalise_height_at_SC_level,
+        "export_average_x": export_average_x,
         "hind_joints": hind_joints,
         "fore_joints": fore_joints,
         "angles": angles,
@@ -727,8 +729,7 @@ def extract_stepcycles(data, info, folderinfo, cfg):
     next_mouse_idx = mouse_row  # search idx of first row of next mouse
 
     # ..............................  main xls read  ...................................
-    # if while is False, we arrived at the next mouse/end & dont update
-    # next_mouse_idx
+    # if while is False, we arrived at the next mouse/end & dont update next_mouse_idx
     # 3 conditions (continue if true):
     # 1) First row of this mouse
     # 2) None means a different run of this mouse or an empty row
@@ -950,7 +951,7 @@ def handle_issues(condition, info):
     elif condition == "no_scs":
         this_message = (
             "\n***********\n! WARNING !\n***********\n"
-            + "Skipped since no SCs in latency XLS!"
+            + "Skipped since no SCs in Annotation Table!"
         )
         print(this_message)
         write_issues_to_textfile(this_message, info)
@@ -958,7 +959,7 @@ def handle_issues(condition, info):
     elif condition == "no_mouse":
         this_message = (
             "\n***********\n! WARNING !\n***********\n"
-            + "Skipped since ID not in latency XLS!"
+            + "Skipped since ID not in Annotation Table!"
         )
         print(this_message)
         write_issues_to_textfile(this_message, info)
@@ -967,7 +968,7 @@ def handle_issues(condition, info):
         this_message = (
             "\n******************\n! CRITICAL ERROR !"
             + "\n******************\n"
-            + "Latency XLS Column names are wrong!\n"
+            + "Annotation Table's Column Names are wrong!\n"
             + "Check Instructions!"
         )
         print(this_message)
@@ -977,7 +978,7 @@ def handle_issues(condition, info):
         this_message = (
             "\n***********\n! WARNING !\n***********\n"
             + "Skipped since ID found more than once in "
-            + "latency XLS!"
+            + "Annotation Table!"
         )
         print(this_message)
         write_issues_to_textfile(this_message, info)
@@ -1007,6 +1008,7 @@ def analyse_and_export_stepcycles(data, all_cycles, info, folderinfo, cfg):
     name = info["name"]
     results_dir = info["results_dir"]
     save_to_xls = cfg["save_to_xls"]
+    export_average_x = cfg["export_average_x"]
     bin_num = cfg["bin_num"]
     # do everything on a copy of the data df
     data_copy = data.copy()
@@ -1052,7 +1054,7 @@ def analyse_and_export_stepcycles(data, all_cycles, info, folderinfo, cfg):
             )
     # compute average & std data
     average_data, std_data = compute_average_and_std_data(
-        name, normalised_steps_data, bin_num, results_dir
+        name, normalised_steps_data, bin_num, export_average_x
     )
     # save to results dict
     results = {}
@@ -1062,15 +1064,23 @@ def analyse_and_export_stepcycles(data, all_cycles, info, folderinfo, cfg):
     results["all_cycles"] = all_cycles
     # save to files
     save_results_sheet(
-        all_steps_data, save_to_xls, results_dir + name + ORIGINAL_XLS_FILENAME
+        all_steps_data,
+        save_to_xls,
+        os.path.join(results_dir, name + ORIGINAL_XLS_FILENAME),
     )
     save_results_sheet(
-        normalised_steps_data, save_to_xls, results_dir + name + NORMALISED_XLS_FILENAME
+        normalised_steps_data,
+        save_to_xls,
+        os.path.join(results_dir, name + NORMALISED_XLS_FILENAME),
     )
     save_results_sheet(
-        average_data, save_to_xls, results_dir + name + AVERAGE_XLS_FILENAME
+        average_data,
+        save_to_xls,
+        os.path.join(results_dir, name + AVERAGE_XLS_FILENAME),
+    )
+    save_results_sheet(
+        std_data, save_to_xls, os.path.join(results_dir, name + STD_XLS_FILENAME)
     )
-    save_results_sheet(std_data, save_to_xls, results_dir + name + STD_XLS_FILENAME)
     return results
 
 
@@ -1253,7 +1263,9 @@ def define_bins(triallength, bin_num):
 # ......................................................................................
 
 
-def compute_average_and_std_data(name, normalised_steps_data, bin_num, results_dir):
+def compute_average_and_std_data(
+    name, normalised_steps_data, bin_num, export_average_x
+):
     """Export XLS tables that store all averages & std of y-coords & angles"""
     # initialise col of % of SC over time for plotting first
     percentages = [int(((s + 1) / bin_num) * 100) for s in range(bin_num)]
@@ -1265,12 +1277,20 @@ def compute_average_and_std_data(name, normalised_steps_data, bin_num, results_d
     )
     sc_num = len(np.where(normalised_steps_data.index == 0)[0])
     for c, col in enumerate(normalised_steps_data.columns):
-        if (
-            (not col.endswith("x"))
-            & (not col.endswith("likelihood"))
-            & (col != TIME_COL)
-            & (col != "Flipped")
-        ):
+        if export_average_x:
+            condition = (
+                (not col.endswith("likelihood"))
+                & (col != TIME_COL)
+                & (col != "Flipped")
+            )
+        else:
+            condition = (
+                (not col.endswith("x"))
+                & (not col.endswith("likelihood"))
+                & (col != TIME_COL)
+                & (col != "Flipped")
+            )
+        if condition:
             this_data = np.zeros([bin_num, sc_num])
             for s in range(sc_num):
                 # with this_end it's bin_num & not bin_num -1 because iloc
@@ -1298,22 +1318,6 @@ def save_results_sheet(dataframe, save_to_xls, fullfilepath):
 # ......................................................................................
 
 
-def delete_previous_xlsfiles(name, results_dir):
-    """
-    Check and delete previously stored excel files (important since appending sheets)
-    """
-    all_filenames = [
-        ORIGINAL_XLS_FILENAME,
-        NORMALISED_XLS_FILENAME,
-        AVERAGE_XLS_FILENAME,
-        STD_XLS_FILENAME,
-    ]
-    for filename in all_filenames:
-        fullfilepath = results_dir + name + filename + ".xlsx"
-        if os.path.exists(fullfilepath):
-            os.remove(fullfilepath)
-
-
 def add_step_separators(dataframe, nanvector, numvector):
     """Add nan & num vector separators between step cycles to dataframes"""
     dataframe = pd.concat([dataframe, nanvector], axis=0)  # nan
@@ -1487,10 +1491,7 @@ def plot_joint_y_by_x(all_steps_data, sc_idxs, info, cfg):
             figure_file_string = " - Foot y by x coordinates"
         else:
             figure_file_string = " - " + joint + "y by x coordinates"
-        f[j].savefig(
-            results_dir + name + figure_file_string + ".png", bbox_inches="tight"
-        )
-        save_as_svg(f[j], results_dir, name, figure_file_string)
+        save_figures(f[j], results_dir, name, figure_file_string)
         if dont_show_plots:
             plt.close(f[j])
 
@@ -1524,11 +1525,8 @@ def plot_angles_by_time(all_steps_data, sc_idxs, info, cfg):
             this_x = all_steps_data.iloc[sc_idxs[s], x_col_idx]
             this_y = all_steps_data.iloc[sc_idxs[s], y_col_idx]
             ax[a].plot(this_x, this_y)
-        figure_file_string = " - " + angle + " Angle by Time"
-        f[a].savefig(
-            results_dir + name + figure_file_string + ".png", bbox_inches="tight"
-        )
-        save_as_svg(f[a], results_dir, name, figure_file_string)
+        figure_file_string = " - " + angle + "Angle by Time"
+        save_figures(f[a], results_dir, name, figure_file_string)
         if dont_show_plots:
             plt.close(f[a])
 
@@ -1590,8 +1588,7 @@ def plot_hindlimb_stickdiagram(all_steps_data, sc_idxs, info, cfg):
         tickconvert_mm_to_cm(ax, "both")
     ax.legend(fontsize=SC_LAT_LEGEND_FONTSIZE)
     figure_file_string = " - Hindlimb Stick Diagram"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1652,8 +1649,7 @@ def plot_forelimb_stickdiagram(all_steps_data, sc_idxs, info, cfg):
         tickconvert_mm_to_cm(ax, "both")
     ax.legend(fontsize=SC_LAT_LEGEND_FONTSIZE)
     figure_file_string = " - Forelimb Stick Diagram"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1693,8 +1689,7 @@ def plot_joint_y_by_average_SC(average_data, std_data, info, cfg):
     if convert_to_mm:
         tickconvert_mm_to_cm(ax, "y")
     figure_file_string = " - Joint y-coord.s over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1731,8 +1726,7 @@ def plot_angles_by_average_SC(average_data, std_data, info, cfg):
         ax.fill_between(x, this_y - this_std, this_y + this_std, alpha=0.2)
     ax.legend()
     figure_file_string = " - Joint angles over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1778,8 +1772,7 @@ def plot_x_velocities_by_average_SC(average_data, std_data, info, cfg):
             "Velocity (x in cm / " + str(int((1 / sampling_rate) * 1000)) + "ms)"
         )
     figure_file_string = " - Joint velocities over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1817,8 +1810,7 @@ def plot_angular_velocities_by_average_SC(average_data, std_data, info, cfg):
         ax.fill_between(x, this_y - this_std, this_y + this_std, alpha=0.2)
     ax.legend()
     figure_file_string = " - Angular velocities over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1864,8 +1856,7 @@ def plot_x_acceleration_by_average_SC(average_data, std_data, info, cfg):
             "Acceleration (x in cm / " + str(int((1 / sampling_rate) * 1000)) + "ms)"
         )
     figure_file_string = " - Joint acceleration over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
@@ -1907,19 +1898,24 @@ def plot_angular_acceleration_by_average_SC(average_data, std_data, info, cfg):
         ax.fill_between(x, this_y - this_std, this_y + this_std, alpha=0.2)
     ax.legend()
     figure_file_string = " - Angular acceleration over average step cycle"
-    f.savefig(results_dir + name + figure_file_string + ".png", bbox_inches="tight")
-    save_as_svg(f, results_dir, name, figure_file_string)
+    save_figures(f, results_dir, name, figure_file_string)
     if dont_show_plots:
         plt.close(f)
 
 
-def save_as_svg(figure, results_dir, name, figure_file_string):
-    """Save figures as svgs to separate subfolder"""
+def save_figures(figure, results_dir, name, figure_file_string):
+    """Save figures as pngs to results_dir and as svgs to separate subfolders"""
+    # pngs to results_dir
+    figure.savefig(
+        os.path.join(results_dir, name + figure_file_string + ".png"),
+        bbox_inches="tight",
+    )
+    # svgs to subfolders
     svg_dir = os.path.join(results_dir, "SVG Figures")
     if not os.path.exists(svg_dir):
         os.makedirs(svg_dir)
     figure.savefig(
-        svg_dir + "/" + name + figure_file_string + ".svg", bbox_inches="tight"
+        os.path.join(svg_dir, name + figure_file_string + ".svg"), bbox_inches="tight"
     )
 
 
@@ -1944,7 +1940,7 @@ def tickconvert_mm_to_cm(axis, whichlabel):
 # %% local functions 5 - print finish
 
 
-def print_finish(cfg):
+def print_finish(info, cfg):
     """Print that we finished this program"""
     # unpack
     dont_show_plots = cfg["dont_show_plots"]
@@ -1953,7 +1949,8 @@ def print_finish(cfg):
         plt.pause(1)  # so we ensure that plots are plotted to python before print
 
     print("\n***************************************************")
-    print("* GAITA FINISHED - RESULTS SAVED IN /Results DIR! *")
+    print("* GAITA FINISHED - RESULTS WERE SAVED HERE:       *")
+    print("* " + info["results_dir"] + " *")
     print("***************************************************")