autogaita 1.0.7__tar.gz → 1.0.8__tar.gz

{autogaita-1.0.7 → autogaita-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.7
+Version: 1.0.8
 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-1.0.7 → autogaita-1.0.8}/autogaita/batchrun_scripts/universal3D_multirun.py

@@ -24,16 +24,11 @@ def universal3D_multirun():
     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["normalise_height_at_SC_level"] = True
     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"],

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/batchrun_scripts/universal3D_singlerun.py

@@ -23,16 +23,11 @@ def universal3D_singlerun():
     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"]
+    cfg["normalise_height_at_SC_level"] = True
     cfg["plot_joint_number"] = 5
     cfg["color_palette"] = "Set2"
     cfg["legend_outside"] = True
-    cfg["flip_gait_direction"] = False
-    cfg["analyse_average_y"] = True
-    cfg["standardise_y_coordinates"] = True
-    cfg["y_standardisation_joint"] = ["Midfoot"]
+    cfg["analyse_average_y"] = False
     cfg["joints"] = [
         # "R1-ThCx",
         "Midfoot",

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/dlc/dlc_1_preparation.py

@@ -169,7 +169,7 @@ 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"]
-    # important to unpack to vars and not to cfg since cfg is overwritten in multiruns!
+    # important to unpack to vars hand not to cfg since cfg is overwritten in multiruns!
     x_standardisation_joint = cfg["x_standardisation_joint"][0]
     y_standardisation_joint = cfg["y_standardisation_joint"][0]
     # store config json file @ group path

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/gui/dlc_gui.py

@@ -198,13 +198,11 @@ def run_dlc_gui():
         WIDGET_CFG,
     )
     convert_checkbox.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "convert_to_mm", ratio_entry
-        ),
+        command=lambda: gui_utils.change_ratio_entry_state(cfg, ratio_entry),
     )
     convert_checkbox.grid(row=2, column=0, columnspan=2, sticky="w")
 
-    # ratio label
+    # ratio  label
     ratio_entry = ctk.CTkEntry(
         root,
         textvariable=cfg["pixel_to_mm_ratio"],
@@ -217,7 +215,7 @@ def run_dlc_gui():
     )
     ratio_right_label.grid(row=2, column=2, sticky="w")
     # to initialise the widget correctly, run this function once
-    gui_utils.change_widget_state_based_on_checkbox(cfg, "convert_to_mm", ratio_entry)
+    gui_utils.change_ratio_entry_state(cfg, ratio_entry)
 
     # subtract beam
     subtract_beam_checkbox = gaita_widgets.checkbox(

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/gui/group_gui.py

@@ -349,7 +349,7 @@ def build_mainwindow(root, group_number, root_dimensions):
         )
         ANOVA_checkbox.configure(
             command=lambda: change_ANOVA_buttons_state(ANOVA_buttons),
-        )  # dont use gui_utils here because its a bit special
+        )
         ANOVA_checkbox.grid(row=last_group_row + 7, column=0, columnspan=3, pady=10)
         # ANOVA design
         ANOVA_string_and_var_value = [

autogaita-1.0.8/autogaita/gui/gui_utils.py

@@ -0,0 +1,92 @@
+import platform
+from importlib import resources
+
+
+# ...............................  general gui stuff  ..................................
+def configure_the_icon(root):
+    """Configure the icon - in macos it changes the dock icon, in windows it changes
+    all windows titlebar icons (taskbar cannot be changed without converting to exe)
+    """
+    if platform.system().startswith("Darwin"):
+        try:
+            from Cocoa import NSApplication, NSImage
+        except ImportError:
+            print("Unable to import pyobjc modules")
+        else:
+            with resources.path("autogaita.resources", "icon.icns") as icon_path:
+                ns_application = NSApplication.sharedApplication()
+                logo_ns_image = NSImage.alloc().initWithContentsOfFile_(str(icon_path))
+                ns_application.setApplicationIconImage_(logo_ns_image)
+    elif platform.system().startswith("win"):
+        with resources.path("autogaita.resources", "icon.ico") as icon_path:
+            root.iconbitmap(str(icon_path))
+
+
+def fix_window_after_its_creation(window):
+    """Perform some quality of life things after creating a window (root or Toplevel)"""
+    window.attributes("-topmost", True)
+    window.focus_set()
+    window.after(100, lambda: window.attributes("-topmost", False))  # 100 ms
+
+
+def maximise_widgets(window):
+    """Maximises all widgets to look good in fullscreen"""
+    # fix the grid to fill the window
+    num_rows = window.grid_size()[1]  # maximise rows
+    for r in range(num_rows):
+        window.grid_rowconfigure(r, weight=1)
+    num_cols = window.grid_size()[0]  # maximise cols
+    for c in range(num_cols):
+        window.grid_columnconfigure(c, weight=1)
+
+
+# ..............................  change widget states  ................................
+def change_ratio_entry_state(cfg, ratio_entry):
+    """Change the state of ratio entry widget based on whether user wants
+    to convert pixels to mm or not.
+    """
+    if cfg["convert_to_mm"].get() is True:
+        ratio_entry.configure(state="normal")
+    elif cfg["convert_to_mm"].get() is False:
+        ratio_entry.configure(state="disabled")
+
+
+def change_y_standardisation_joint_entry_state(cfg, y_standardisation_joint_entry):
+    if cfg["standardise_y_to_a_joint"].get() is True:
+        y_standardisation_joint_entry.configure(state="normal")
+    elif cfg["standardise_y_to_a_joint"].get() is False:
+        y_standardisation_joint_entry.configure(state="disabled")
+
+
+def change_x_standardisation_box_state(cfg, standardise_x_coordinates_box):
+    if cfg["analyse_average_x"].get() is True:
+        standardise_x_coordinates_box.configure(state="normal")
+    elif cfg["analyse_average_x"].get() is False:
+        standardise_x_coordinates_box.configure(state="disabled")
+
+
+def change_x_standardisation_joint_entry_state(cfg, x_standardisation_joint_entry):
+    if cfg["standardise_x_coordinates"].get() is True:
+        x_standardisation_joint_entry.configure(state="normal")
+    elif cfg["standardise_x_coordinates"].get() is False:
+        x_standardisation_joint_entry.configure(state="disabled")
+
+
+def change_ID_entry_state(cfg, ID_entry):
+    """Change the state of ID entry widget based on whether user wants to only analyse
+    a single dataset.
+    """
+    if cfg["analyse_singlerun"].get() is True:
+        ID_entry.configure(state="normal")
+    elif cfg["analyse_singlerun"].get() is False:
+        ID_entry.configure(state="disabled")
+
+
+def change_postname_entry_state(results, postname_entry):
+    """Change the state of ID entry widget based on whether user wants to only analyse
+    a single dataset.
+    """
+    if results["postname_flag"].get() is True:
+        postname_entry.configure(state="normal")
+    elif results["postname_flag"].get() is False:
+        postname_entry.configure(state="disabled")

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/gui/sleap_gui.py

@@ -192,9 +192,7 @@ def run_sleap_gui():
         WIDGET_CFG,
     )
     convert_checkbox.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "convert_to_mm", ratio_entry
-        ),
+        command=lambda: gui_utils.change_ratio_entry_state(cfg, ratio_entry),
     )
     convert_checkbox.grid(row=2, column=0, columnspan=2, sticky="w")
 
@@ -211,7 +209,7 @@ def run_sleap_gui():
     )
     ratio_right_label.grid(row=2, column=2, sticky="w")
     # to initialise the widget correctly, run this function once
-    gui_utils.change_widget_state_based_on_checkbox(cfg, "convert_to_mm", ratio_entry)
+    gui_utils.change_ratio_entry_state(cfg, ratio_entry)
 
     # NU - I'll implement beam subtraction and gait direction flipping after having
     #      data for testing

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/gui/universal3D_gui.py

@@ -42,7 +42,7 @@ WIDGET_CFG["HOVER_COLOR"] = HOVER_COLOR
 
 CONFIG_FILE_NAME = "universal3D_gui_config.json"
 INT_VARS = ["sampling_rate", "bin_num", "plot_joint_number"]
-LIST_VARS = ["joints", "y_standardisation_joint", "z_standardisation_joint"]
+LIST_VARS = ["joints"]
 DICT_VARS = ["angles"]
 # TK_BOOL/STR_VARS are only used for initialising widgets based on cfg file
 # (note that numbers are initialised as strings)
@@ -52,11 +52,8 @@ TK_BOOL_VARS = [
     "y_acceleration",
     "angular_acceleration",
     "plot_SE",
-    "standardise_z_at_SC_level",
-    "standardise_z_to_a_joint",
-    "standardise_y_coordinates",
+    "normalise_height_at_SC_level",
     "postname_flag",
-    "flip_gait_direction",
     "analyse_average_y",
     "legend_outside",
     "fileprep_3D_DLC",
@@ -193,15 +190,6 @@ def run_universal3D_gui():
     samprate_label.grid(row=3, column=0, columnspan=2, sticky="w")
     samprate_entry.grid(row=3, column=1)
 
-    # flip gait direction
-    flip_gait_direction_box = gaita_widgets.checkbox(
-        root,
-        "Standardise direction of movement across runs",
-        cfg["flip_gait_direction"],
-        WIDGET_CFG,
-    )
-    flip_gait_direction_box.grid(row=4, column=0, columnspan=2, sticky="w")
-
     # postname present checkbox
     postname_flag_checkbox = gaita_widgets.checkbox(
         root,
@@ -210,11 +198,9 @@ def run_universal3D_gui():
         WIDGET_CFG,
     )
     postname_flag_checkbox.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            results, "postname_flag", postname_entry
-        ),
+        command=lambda: gui_utils.change_postname_entry_state(results, postname_entry),
     )
-    postname_flag_checkbox.grid(row=5, column=0, columnspan=2)
+    postname_flag_checkbox.grid(row=4, column=0, columnspan=2)
 
     # postname string
     postname_label, postname_entry = gaita_widgets.label_and_entry_pair(
@@ -223,13 +209,13 @@ def run_universal3D_gui():
         results["postname_string"],
         WIDGET_CFG,
     )
-    postname_label.grid(row=6, column=0, sticky="e")
+    postname_label.grid(row=5, column=0, sticky="e")
     postname_entry.configure(state="disabled")
-    postname_entry.grid(row=6, column=1, sticky="w")
+    postname_entry.grid(row=5, column=1, sticky="w")
 
     # empty label 1 (for spacing)
     empty_label_one = ctk.CTkLabel(root, text="")
-    empty_label_one.grid(row=7, column=0)
+    empty_label_one.grid(row=8, column=0)
 
     # ..........................  advanced cfg section  ................................
 
@@ -237,7 +223,7 @@ def run_universal3D_gui():
     advanced_cfg_header_label = gaita_widgets.header_label(
         root, "Advanced Configuration", WIDGET_CFG
     )
-    advanced_cfg_header_label.grid(row=8, column=0, columnspan=2, sticky="nsew")
+    advanced_cfg_header_label.grid(row=9, column=0, columnspan=2, sticky="nsew")
 
     # data file preparation window
     datafile_prep_button = gaita_widgets.header_button(
@@ -246,7 +232,7 @@ def run_universal3D_gui():
     datafile_prep_button.configure(
         command=lambda: build_datafile_prep_window(root, results, cfg),
     )
-    datafile_prep_button.grid(row=9, column=0, columnspan=2)
+    datafile_prep_button.grid(row=10, column=0, columnspan=2)
 
     # column name information window
     column_info_button = gaita_widgets.header_button(
@@ -255,7 +241,7 @@ def run_universal3D_gui():
     column_info_button.configure(
         command=lambda: build_column_info_window(root, cfg, root_dimensions),
     )
-    column_info_button.grid(row=10, column=0, columnspan=2)
+    column_info_button.grid(row=11, column=0, columnspan=2)
 
     # advanced cfg
     cfg_window_button = gaita_widgets.header_button(
@@ -264,17 +250,17 @@ def run_universal3D_gui():
     cfg_window_button.configure(
         command=lambda: (build_cfg_window(root, cfg)),
     )
-    cfg_window_button.grid(row=11, column=0, columnspan=2)
+    cfg_window_button.grid(row=12, column=0, columnspan=2)
 
     # empty label 2 (for spacing)
     empty_label_two = ctk.CTkLabel(root, text="")
-    empty_label_two.grid(row=12, column=0)
+    empty_label_two.grid(row=13, column=0)
 
     # ............................  run & exit section  ................................
 
     # run analysis label
     runheader_label = gaita_widgets.header_label(root, "Run Analysis", WIDGET_CFG)
-    runheader_label.grid(row=13, column=0, columnspan=2, sticky="nsew")
+    runheader_label.grid(row=14, column=0, columnspan=2, sticky="nsew")
 
     # single video checkbox
     singlevideo_checkbox = gaita_widgets.checkbox(
@@ -284,19 +270,17 @@ def run_universal3D_gui():
         WIDGET_CFG,
     )
     singlevideo_checkbox.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "analyse_singlerun", ID_entry
-        ),
+        command=lambda: gui_utils.change_ID_entry_state(cfg, ID_entry),
     )
-    singlevideo_checkbox.grid(row=14, column=0, columnspan=2)
+    singlevideo_checkbox.grid(row=15, column=0, columnspan=2)
 
     # ID string info
     ID_label, ID_entry = gaita_widgets.label_and_entry_pair(
         root, "ID to be analysed:", results["name"], WIDGET_CFG
     )
-    ID_label.grid(row=15, column=0, sticky="e")
-    ID_entry.grid(row=15, column=1, sticky="w")
-    gui_utils.change_widget_state_based_on_checkbox(cfg, "analyse_singlerun", ID_entry)
+    ID_label.grid(row=16, column=0, sticky="e")
+    ID_entry.grid(row=16, column=1, sticky="w")
+    gui_utils.change_ID_entry_state(cfg, ID_entry)
 
     # run analysis button
     run_button = gaita_widgets.header_button(root, "Run Analysis!", WIDGET_CFG)
@@ -315,11 +299,11 @@ def run_universal3D_gui():
             build_donewindow(results, root, root_dimensions),
         )
     )
-    run_button.grid(row=16, column=0, columnspan=2, padx=10, pady=(10, 5))
+    run_button.grid(row=17, column=0, columnspan=2, padx=10, pady=(10, 5))
 
     # empty label 3 (for spacing)
     empty_label_three = ctk.CTkLabel(root, text="")
-    empty_label_three.grid(row=17, column=0)
+    empty_label_three.grid(row=18, column=0)
 
     # close program button
     exit_button = gaita_widgets.exit_button(
@@ -342,7 +326,7 @@ def run_universal3D_gui():
             root.after(5000, root.destroy),
         ),
     )
-    exit_button.grid(row=18, column=0, columnspan=2, padx=10, pady=(10, 5))
+    exit_button.grid(row=19, column=0, columnspan=2, padx=10, pady=(10, 5))
 
     # maximise widgets
     gui_utils.maximise_widgets(root)
@@ -572,9 +556,7 @@ def build_cfg_window(root, cfg):
     adv_cfg_analysis_header_label = gaita_widgets.header_label(
         cfg_window, "Analysis", WIDGET_CFG
     )
-    adv_cfg_analysis_header_label.grid(
-        row=0, column=0, rowspan=2, columnspan=2, sticky="nsew"
-    )
+    adv_cfg_analysis_header_label.grid(row=0, column=0, rowspan=2, sticky="nsew")
     # bin_num
     bin_num_label, bin_num_entry = gaita_widgets.label_and_entry_pair(
         cfg_window,
@@ -583,73 +565,35 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    bin_num_label.grid(row=2, column=0, columnspan=2)
-    bin_num_entry.grid(row=3, column=0, columnspan=2)
-    # acceleration label
-    acceleration_string = "Analyse (i.e. plot & export) accelerations for:"
-    acceleration_label = ctk.CTkLabel(
-        cfg_window,
-        text=acceleration_string,
-        font=(TEXT_FONT_NAME, ADV_CFG_TEXT_FONT_SIZE),
-    )
-    acceleration_label.grid(row=4, column=0, columnspan=2)
+    bin_num_label.grid(row=2, column=0)
+    bin_num_entry.grid(row=3, column=0)
     # y acceleration
     y_accel_box = gaita_widgets.checkbox(
         cfg_window,
-        "y-coordinates",
+        "Compute, plot & export joints' Y-accelerations",
         cfg["y_acceleration"],
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    y_accel_box.grid(row=5, column=0, sticky="e")
+    y_accel_box.grid(row=4, column=0)
     # angular acceleration
     angular_accel_box = gaita_widgets.checkbox(
         cfg_window,
-        "angles",
+        "Compute, plot & export angular accelerations",
         cfg["angular_acceleration"],
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    angular_accel_box.grid(row=5, column=1, sticky="w")
-    # height standardisation at each step cycle separately
-    z_standardisation_box = gaita_widgets.checkbox(
-        cfg_window,
-        "Normalise heights separately for all step cycles",
-        cfg["standardise_z_at_SC_level"],
-        WIDGET_CFG,
-        adv_cfg_textsize=True,
-    )
-    z_standardisation_box.grid(row=6, column=0, columnspan=2)
-    # z standardisation to a specific joint not global minimum
-    standardise_z_to_joint_box = gaita_widgets.checkbox(
+    angular_accel_box.grid(row=5, column=0)
+    # height normalisation at each step cycle separately
+    height_normalisation_box = gaita_widgets.checkbox(
         cfg_window,
-        "Standardise heights to a joint instead of to global minimum",
-        cfg["standardise_z_to_a_joint"],
+        "Normalise heights of all step cycles separately",
+        cfg["normalise_height_at_SC_level"],
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    standardise_z_to_joint_box.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "standardise_z_to_a_joint", z_standardisation_joint_entry
-        ),
-    )
-    standardise_z_to_joint_box.grid(row=7, column=0, columnspan=2)
-    # z standardisation joint string label & entry
-    z_standardisation_joint_label, z_standardisation_joint_entry = (
-        gaita_widgets.label_and_entry_pair(
-            cfg_window,
-            "Height-standardisation joint:",
-            cfg["z_standardisation_joint"][0],
-            WIDGET_CFG,
-            adv_cfg_textsize=True,
-        )
-    )
-    z_standardisation_joint_label.grid(row=8, column=0, sticky="e")
-    z_standardisation_joint_entry.grid(row=8, column=1, sticky="w")
-    # to initialise the widget correctly, run this function once
-    gui_utils.change_widget_state_based_on_checkbox(
-        cfg, "standardise_z_to_a_joint", z_standardisation_joint_entry
-    )
+    height_normalisation_box.grid(row=6, column=0)
     # export average y coordinates
     analyse_average_y_box = gaita_widgets.checkbox(
         cfg_window,
@@ -658,53 +602,14 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    analyse_average_y_box.grid(row=9, column=0, columnspan=2)
-    analyse_average_y_box.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "analyse_average_y", standardise_y_coordinates_box
-        ),
-    )
-    # standardise y coordinates
-    standardise_y_coordinates_box = gaita_widgets.checkbox(
-        cfg_window,
-        "Standardise y-coordinates",
-        cfg["standardise_y_coordinates"],
-        WIDGET_CFG,
-        adv_cfg_textsize=True,
-    )
-    standardise_y_coordinates_box.configure(
-        command=lambda: gui_utils.change_widget_state_based_on_checkbox(
-            cfg, "standardise_y_coordinates", y_standardisation_joint_entry
-        ),
-    )
-    standardise_y_coordinates_box.grid(row=10, column=0, columnspan=2)
-    gui_utils.change_widget_state_based_on_checkbox(
-        cfg, "analyse_average_y", standardise_y_coordinates_box
-    )
-    # y standardisation joint string label & entry
-    y_standardisation_joint_label, y_standardisation_joint_entry = (
-        gaita_widgets.label_and_entry_pair(
-            cfg_window,
-            "Y-standardisation joint:",
-            cfg["y_standardisation_joint"][0],
-            WIDGET_CFG,
-            adv_cfg_textsize=True,
-        )
-    )
-    y_standardisation_joint_label.grid(row=11, column=0, sticky="e")
-    y_standardisation_joint_entry.grid(row=11, column=1, sticky="w")
-    gui_utils.change_widget_state_based_on_checkbox(
-        cfg, "standardise_y_coordinates", y_standardisation_joint_entry
-    )
+    analyse_average_y_box.grid(row=7, column=0)
 
     #  .............................  advanced output  .................................
     # advanced output header
     adv_cfg_output_header_label = gaita_widgets.header_label(
         cfg_window, "Output", WIDGET_CFG
     )
-    adv_cfg_output_header_label.grid(
-        row=12, column=0, rowspan=2, columnspan=2, sticky="nsew"
-    )
+    adv_cfg_output_header_label.grid(row=8, column=0, rowspan=2, sticky="nsew")
     # number of joints to plot
     plot_joint_num_label, plot_joint_num_entry = gaita_widgets.label_and_entry_pair(
         cfg_window,
@@ -713,8 +618,8 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    plot_joint_num_label.grid(row=14, column=0, sticky="e")
-    plot_joint_num_entry.grid(row=14, column=1, sticky="w")
+    plot_joint_num_label.grid(row=10, column=0)
+    plot_joint_num_entry.grid(row=11, column=0)
     # plot plots to python
     showplots_checkbox = gaita_widgets.checkbox(
         cfg_window,
@@ -723,7 +628,7 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    showplots_checkbox.grid(row=15, column=0, columnspan=2)
+    showplots_checkbox.grid(row=12, column=0)
     # plot SE
     plot_SE_box = gaita_widgets.checkbox(
         cfg_window,
@@ -732,7 +637,7 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    plot_SE_box.grid(row=16, column=0, columnspan=2)
+    plot_SE_box.grid(row=13, column=0)
     # color palette
     color_palette_string = "Choose figures' color palette"
     color_palette_label = ctk.CTkLabel(
@@ -740,7 +645,7 @@ def build_cfg_window(root, cfg):
         text=color_palette_string,
         font=(TEXT_FONT_NAME, ADV_CFG_TEXT_FONT_SIZE),
     )
-    color_palette_label.grid(row=17, column=0, columnspan=2)
+    color_palette_label.grid(row=14, column=0)
     color_palette_entry = ctk.CTkOptionMenu(
         cfg_window,
         values=COLOR_PALETTES_LIST,
@@ -750,7 +655,7 @@ def build_cfg_window(root, cfg):
         button_hover_color=HOVER_COLOR,
         font=(TEXT_FONT_NAME, ADV_CFG_TEXT_FONT_SIZE),
     )
-    color_palette_entry.grid(row=18, column=0, columnspan=2)
+    color_palette_entry.grid(row=15, column=0)
     # legend outside
     legend_outside_checkbox = gaita_widgets.checkbox(
         cfg_window,
@@ -759,7 +664,7 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    legend_outside_checkbox.grid(row=19, column=0, columnspan=2)
+    legend_outside_checkbox.grid(row=16, column=0)
 
     # results dir
     results_dir_label, results_dir_entry = gaita_widgets.label_and_entry_pair(
@@ -769,8 +674,8 @@ def build_cfg_window(root, cfg):
         WIDGET_CFG,
         adv_cfg_textsize=True,
     )
-    results_dir_label.grid(row=20, column=0, columnspan=2)
-    results_dir_entry.grid(row=21, column=0, columnspan=2)
+    results_dir_label.grid(row=17, column=0)
+    results_dir_entry.grid(row=18, column=0)
 
     # done button
     adv_cfg_done_button = ctk.CTkButton(
@@ -782,10 +687,10 @@ def build_cfg_window(root, cfg):
         command=lambda: cfg_window.destroy(),
     )
     adv_cfg_done_button.grid(
-        row=22, column=0, rowspan=2, columnspan=2, sticky="nsew", padx=10, pady=(10, 5)
+        row=19, column=0, rowspan=2, sticky="nsew", padx=10, pady=(10, 5)
     )
     # maximise widgets
-    cfg_window.columnconfigure(list(range(2)), weight=1, uniform="Silent_Creme")
+    cfg_window.columnconfigure(0, weight=1, uniform="Silent_Creme")
     cfg_window.rowconfigure(list(range(20)), weight=1, uniform="Silent_Creme")
 
 

{autogaita-1.0.7 → autogaita-1.0.8}/autogaita/gui/universal3D_gui_config.json

@@ -15,17 +15,8 @@
         "bin_num": "25",
         "plot_joint_number": "3",
         "plot_SE": false,
-        "standardise_z_at_SC_level": false,
-        "standardise_z_to_a_joint": true,
-        "z_standardisation_joint": [
-            "Ankle"
-        ],
-        "flip_gait_direction": true,
+        "normalise_height_at_SC_level": false,
         "analyse_average_y": true,
-        "standardise_y_coordinates": true,
-        "y_standardisation_joint": [
-            "Ankle"
-        ],
         "color_palette": "Set2",
         "legend_outside": true,
         "results_dir": "",