autogaita 0.3.0__tar.gz → 0.3.1__tar.gz

autogaita-0.3.1/PKG-INFO

@@ -0,0 +1,10 @@
+Metadata-Version: 2.1
+Name: autogaita
+Version: 0.3.1
+Summary: Automatic Gait Analysis in Python
+Home-page: https://github.com/mahan-hosseini/AutoGaitA/
+Author: Mahan Hosseini
+License: GPLv3
+Requires-Python: >=3.10
+Provides-Extra: dev
+License-File: LICENSE

{autogaita-0.3.0 → autogaita-0.3.1}/README.md

@@ -31,7 +31,7 @@ It is strongly recommended that a separate virtual environment for AutoGaitA is
 
 - Access the main user interface via `python -m autogaita`.
 
-- To update to the latest release (see the *Releases* panel on the right for the current version) activate your virtual environment & enter `pip install autogaita -U`. 
+- 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
 

{autogaita-0.3.0 → autogaita-0.3.1}/autogaita/autogaita_dlc.py

@@ -84,6 +84,8 @@ def dlc(info, folderinfo, cfg):
     all_cycles = extract_stepcycles(data, info, folderinfo, cfg)
     if not all_cycles:
         handle_issues("scs_invalid", info)
+        if cfg["dont_show_plots"] is False:  # otherwise stuck at loading
+            plot_panel_instance.destroy_plot_panel()
         return
 
     # .........  main analysis: sc-lvl y-norm, features, df-creation & export ..........
@@ -1443,6 +1445,9 @@ def plot_results(info, results, folderinfo, cfg, plot_panel_instance):
     # ...............................3 - angles by time.................................
     if angles["name"]:
         plot_angles_by_time(all_steps_data, sc_idxs, info, cfg, plot_panel_instance)
+    # regularly closing figures to save memory
+    # => no problem to do this since we pass figure-vars to save-functions and PlotPanel
+    plt.close("all")
 
     # ..........................4 - hindlimb stick diagram..............................
     plot_hindlimb_stickdiagram(all_steps_data, sc_idxs, info, cfg, plot_panel_instance)
@@ -1461,6 +1466,7 @@ def plot_results(info, results, folderinfo, cfg, plot_panel_instance):
         plot_joint_x_by_average_SC(
             average_data, std_data, info, cfg, plot_panel_instance
         )
+    plt.close("all")
 
     # ........................8 - average angles over SC percentage.....................
     if angles["name"]:
@@ -1491,11 +1497,12 @@ def plot_results(info, results, folderinfo, cfg, plot_panel_instance):
             plot_angular_acceleration_by_average_SC(
                 average_data, std_data, info, cfg, plot_panel_instance
             )
+    plt.close("all")
 
     # ........................optional - 13 - build plot panel..........................
-    if cfg["dont_show_plots"] is True:
+    if dont_show_plots is True:
         pass  # going on without building the plot window
-    elif cfg["dont_show_plots"] is False:  # -> show plot panel
+    elif dont_show_plots is False:  # -> show plot panel
         # Destroy loading screen and build plot panel with all figures
         plot_panel_instance.destroy_plot_panel_loading_screen()
         plot_panel_instance.build_plot_panel()
@@ -2427,6 +2434,10 @@ class PlotPanel:
             f"AutoGaitA Plot Panel {self.current_fig_index+1}/{len(self.figures)}"
         )
 
+    def destroy_plot_panel(self):
+        # Needed if no SCs after checks
+        self.loading_screen.destroy()
+
 
 # %% local functions 5 - print finish
 

{autogaita-0.3.0 → autogaita-0.3.1}/autogaita/autogaita_group.py

@@ -135,6 +135,7 @@ def group(folderinfo, cfg):
     # ...................................  PCA  ........................................
     if cfg["PCA_variables"]:  # empty lists are falsey!
         PCA_on_a_limb(avg_dfs, folderinfo, cfg, plot_panel_instance)
+    plt.close("all")  # OK since all figures passed to save-funcs & PlotPanel
 
     # ..............................  prepare statistics  ..............................
     stats_df = create_stats_df(avg_dfs, folderinfo, cfg)
@@ -152,6 +153,7 @@ def group(folderinfo, cfg):
                     cfg,
                     plot_panel_instance,
                 )
+        plt.close("all")
 
         # ..................................  ANOVA  ...................................
         if cfg["do_anova"]:  # indentation since we check for stats-vars here too!
@@ -165,6 +167,7 @@ def group(folderinfo, cfg):
                     cfg,
                     plot_panel_instance,
                 )
+        plt.close("all")
 
     # ..................................  plots  .......................................
     plot_results(g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance)
@@ -606,6 +609,10 @@ def import_and_combine_dfs(
                 group_df = df_copy.iloc[sc_idxs[sc]]
             else:
                 nanvector = df_copy.loc[[1]]
+                # new for pandas 2.2.2 - change all cols to floats so its compatible
+                # with np.nan concatenation (does this break anything?)
+                # pdb.set_trace()
+                nanvector = nanvector.astype(float)
                 nanvector[:] = np.nan
                 group_df = pd.concat([group_df, nanvector], axis=0)
                 group_df = pd.concat([group_df, df_copy.iloc[sc_idxs[sc]]], axis=0)
@@ -1124,7 +1131,6 @@ def plot_PCA(PCA_df, PCA_info, folderinfo, cfg, plot_panel_instance):
             )
             writervideo = FFMpegWriter(fps=30)  # save to m4 using ffmpeg writer
             anim.save(results_dir + "PCA 3D Scatterplot.mp4", writer=writervideo)
-            plt.close()
 
 
 # %% ................  local functions #5 - prepare statistics  ........................
@@ -1507,7 +1513,6 @@ def plot_permutation_test_results(
     f.suptitle(figure_file_string, fontsize=PERM_PLOT_SUPLABEL_SIZE)
     save_figures(f, results_dir, figure_file_string)
 
-    plt.close(f)
     # add figure to plot panel figures list
     if dont_show_plots is False:  # -> show plot panel
         plot_panel_instance.figures.append(f)
@@ -1790,7 +1795,6 @@ def plot_multcomp_results(
     )
     save_figures(f, results_dir, figure_file_string)
 
-    plt.close(f)
     # add figure to plot panel figures list
     if dont_show_plots is False:  # -> show plot panel
         plot_panel_instance.figures.append(f)
@@ -1834,6 +1838,7 @@ def plot_results(g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance):
     plot_joint_y_by_average_SC(
         g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance
     )
+    plt.close("all")
 
     # .......................2 - x coords over average SC (optional)....................
     if tracking_software == "DLC":
@@ -1846,23 +1851,27 @@ def plot_results(g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance):
         plot_joint_x_by_average_SC(
             g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance
         )
+        plt.close("all")
 
     # ........................3 - angles over average SC................................
     if angles["name"]:
         plot_angles_by_average_SC(
             g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance
         )
+        plt.close("all")
 
     # .................4 - average x velocities over SC percentage......................
     plot_x_velocities_by_average_SC(
         g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance
     )
+    plt.close("all")
 
     # ..............5 - average angular velocities over SC percentage...................
     if angles["name"]:
         plot_angular_velocities_by_average_SC(
             g_avg_dfs, g_std_dfs, folderinfo, cfg, plot_panel_instance
         )
+        plt.close("all")
 
     # ........................optional - 6 - build plot panel..........................
     if cfg["dont_show_plots"] is True:
@@ -1931,7 +1940,6 @@ def plot_joint_y_by_average_SC(
             ax.set_ylabel("Z")
             figure_file_string = " - Joint Z-coord.s over average step cycle"
         save_figures(f, results_dir, group_name + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -1980,7 +1988,6 @@ def plot_joint_y_by_average_SC(
             ax.set_ylabel("Z")
             figure_file_string = "- Z-coord.s over average step cycle"
         save_figures(f, results_dir, joint + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2045,7 +2052,6 @@ def plot_joint_x_by_average_SC(
             ax.set_ylabel("Y")
             figure_file_string = " - Joint Y-coord.s over average step cycle"
         save_figures(f, results_dir, group_name + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2094,7 +2100,6 @@ def plot_joint_x_by_average_SC(
             ax.set_ylabel("Y")
             figure_file_string = "- Y-coord.s over average step cycle"
         save_figures(f, results_dir, joint + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2153,7 +2158,6 @@ def plot_angles_by_average_SC(
             )
         figure_file_string = " - Joint angles over average step cycle"
         save_figures(f, results_dir, group_name + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2195,7 +2199,6 @@ def plot_angles_by_average_SC(
             ax.set_title(title_leg + " " + angle + " angle over average step cycle")
         figure_file_string = " - Angle over average step cycle"
         save_figures(f, results_dir, angle + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2275,7 +2278,6 @@ def plot_x_velocities_by_average_SC(
             )
         figure_file_string = " - Joint velocities over average step cycle"
         save_figures(f, results_dir, group_name + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2336,7 +2338,6 @@ def plot_x_velocities_by_average_SC(
             )
         figure_file_string = "- Velocities over average step cycle"
         save_figures(f, results_dir, joint + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2400,7 +2401,6 @@ def plot_angular_velocities_by_average_SC(
             )
         figure_file_string = " - Angular velocities over average step cycle"
         save_figures(f, results_dir, group_name + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel
@@ -2449,7 +2449,6 @@ def plot_angular_velocities_by_average_SC(
             )
         figure_file_string = " - Angular Velocities over average step cycle"
         save_figures(f, results_dir, angle + figure_file_string)
-        plt.close(f)
 
         # add figure to plot panel figures list
         if dont_show_plots is False:  # -> show plot panel

{autogaita-0.3.0 → autogaita-0.3.1}/autogaita/autogaita_simi.py

@@ -116,6 +116,8 @@ def simi(info, folderinfo, cfg):
     all_cycles = extract_stepcycles(data, info, folderinfo, cfg)
     all_cycles = check_stepcycles(all_cycles, info)
     if not all_cycles:  # only None if both leg's SCs were None
+        if cfg["dont_show_plots"] is False:  # otherwise stuck at loading
+            plot_panel_instance.destroy_plot_panel()
         return
 
     # ......  main analysis: y-flipping, features, df-creation & exports  ..............
@@ -1539,6 +1541,10 @@ def plot_results(results, all_cycles, info, cfg, plot_panel_instance):
     angles = cfg["angles"]
     y_acceleration = cfg["y_acceleration"]
     angular_acceleration = cfg["angular_acceleration"]
+    analyse_average_y = cfg["analyse_average_y"]
+    dont_show_plots = cfg["dont_show_plots"]
+    if dont_show_plots:
+        plt.switch_backend("Agg")
 
     # unpack - output specific vars (results to be plotted)
     for legname in LEGS:  # !!! NU - output...
@@ -1553,15 +1559,19 @@ def plot_results(results, all_cycles, info, cfg, plot_panel_instance):
         )
 
         # ........................  2 - y coords by time  ..............................
-        plot_joint_y_by_time(
-            legname, all_steps_data, all_cycles, info, cfg, plot_panel_instance
-        )
+        if analyse_average_y:
+            plot_joint_y_by_time(
+                legname, all_steps_data, all_cycles, info, cfg, plot_panel_instance
+            )
 
         # ..................  3 - angle by time for each SC  ...........................
         if angles["name"]:
             plot_angles_by_time(
                 legname, all_steps_data, all_cycles, info, cfg, plot_panel_instance
             )
+        # regularly closing figures to save memory
+        # => no problem to do this since we pass figure-vars to save-functions and Panel
+        plt.close("all")
 
         # ............................  4 - stick diagram  .............................
         plot_stickdiagram(
@@ -1574,15 +1584,17 @@ def plot_results(results, all_cycles, info, cfg, plot_panel_instance):
         )
 
         # .................  5 - average 5-joints' y over SC percentage  ...............
-        plot_joint_y_by_average_SC(
-            legname, average_data, std_data, sc_num, info, cfg, plot_panel_instance
-        )
+        if analyse_average_y:
+            plot_joint_y_by_average_SC(
+                legname, average_data, std_data, sc_num, info, cfg, plot_panel_instance
+            )
 
         # ...................  6 - average angles over SC percentage  ..................
         if angles["name"]:
             plot_angles_by_average_SC(
                 legname, average_data, std_data, sc_num, info, cfg, plot_panel_instance
             )
+        plt.close("all")
 
         # .............  7 - average y velocities over SC percentage   .................
         plot_y_velocities_by_average_SC(
@@ -1613,11 +1625,12 @@ def plot_results(results, all_cycles, info, cfg, plot_panel_instance):
                     cfg,
                     plot_panel_instance,
                 )
+        plt.close("all")
 
     # ........................optional - 11 - build plot panel..........................
-    if cfg["dont_show_plots"] is True:
+    if dont_show_plots is True:
         pass  # going on without building the plot window
-    elif cfg["dont_show_plots"] is False:  # -> show plot panel
+    elif dont_show_plots is False:  # -> show plot panel
         # Destroy loading screen and build plot panel with all figures
         plot_panel_instance.destroy_plot_panel_loading_screen()
         plot_panel_instance.build_plot_panel()
@@ -2597,6 +2610,10 @@ class PlotPanel:
             f"AutoGaitA Plot Panel {self.current_fig_index+1}/{len(self.figures)}"
         )
 
+    def destroy_plot_panel(self):
+        # Needed if no SCs after checks
+        self.loading_screen.destroy()
+
 
 # %% local functions 5 - print finish
 

{autogaita-0.3.0 → autogaita-0.3.1}/autogaita/batchrun_scripts/autogaita_dlc_multirun.py

@@ -95,16 +95,39 @@ def extract_info(folderinfo):
     postrun_string = folderinfo["postrun_string"]
     info = {"name": [], "mouse_num": [], "run_num": []}
     for filename in os.listdir(folderinfo["root_dir"]):
+        # make sure we don't get wrong files
         if (
-            (premouse_string in filename)  # make sure we don't get wrong files
+            (premouse_string in filename)
             & (prerun_string in filename)
             & (filename.endswith(".csv"))
         ):
-            # we can use COUNT vars as we do here, since we start @ 0 and do
-            # not include the last index (so if counts=2, idx=[0:2]=include
-            # 0&1 only!)
-            this_mouse_num = find_number(filename, premouse_string, postmouse_string)
-            this_run_num = find_number(filename, prerun_string, postrun_string)
+            # ID number - fill in "_" for user if needed
+            this_mouse_num = False
+            for candidate_postmouse_string in [
+                postmouse_string,
+                "_" + postmouse_string,
+            ]:
+                try:
+                    this_mouse_num = find_number(
+                        filename,
+                        premouse_string,
+                        candidate_postmouse_string,
+                    )
+                except:
+                    pass
+            # Do the same for run number
+            this_run_num = False
+            for candidate_postrun_string in [
+                postrun_string,
+                "-" + postrun_string,
+            ]:
+                try:
+                    this_run_num = find_number(
+                        filename, prerun_string, candidate_postrun_string
+                    )
+                except:
+                    pass
+            # if we found both an ID and a run number, create this_name & add to dict
             this_name = "ID " + str(this_mouse_num) + " - Run " + str(this_run_num)
             if this_name not in info["name"]:  # no data/beam duplicates here
                 info["name"].append(this_name)

autogaita-0.3.1/autogaita.egg-info/PKG-INFO

@@ -0,0 +1,10 @@
+Metadata-Version: 2.1
+Name: autogaita
+Version: 0.3.1
+Summary: Automatic Gait Analysis in Python
+Home-page: https://github.com/mahan-hosseini/AutoGaitA/
+Author: Mahan Hosseini
+License: GPLv3
+Requires-Python: >=3.10
+Provides-Extra: dev
+License-File: LICENSE

{autogaita-0.3.0 → autogaita-0.3.1}/setup.py

@@ -25,7 +25,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="0.3.0",  # rc == release candidate (before release is finished)
+    version="0.3.1",  # rc == release candidate (before release is finished)
     author="Mahan Hosseini",
     description="Automatic Gait Analysis in Python",
     packages=["autogaita", "autogaita.batchrun_scripts"],

autogaita-0.3.0/PKG-INFO

@@ -1,24 +0,0 @@
-Metadata-Version: 2.1
-Name: autogaita
-Version: 0.3.0
-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: seaborn>=0.13
-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-0.3.0/autogaita.egg-info/PKG-INFO

@@ -1,24 +0,0 @@
-Metadata-Version: 2.1
-Name: autogaita
-Version: 0.3.0
-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: seaborn>=0.13
-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-0.3.0 → autogaita-0.3.1}/autogaita/batchrun_scripts/autogaita_dlc_singlerun.py

@@ -11,8 +11,8 @@ def dlc_singlerun():
     # folderinfo
     folderinfo = {}
     folderinfo["root_dir"] = "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/"
-    folderinfo["results_dir"] = ""
     folderinfo["sctable_filename"] = "25mm.xlsx"
+    folderinfo["results_dir"] = ""
     folderinfo["data_string"] = "SIMINewOct"
     folderinfo["beam_string"] = "BeamTraining"
     folderinfo["premouse_string"] = "Mouse"