autogaita 1.1.0__tar.gz → 1.1.1__tar.gz

{autogaita-1.1.0 → autogaita-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.1.0
+Version: 1.1.1
 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-1.1.0 → autogaita-1.1.1}/README.md

@@ -11,7 +11,7 @@
 
 # Automated Gait Analysis in Python 🐸
 
-- AutoGaitA simplifies, accelerates, and standardises gait analyses after body posture tracking in 2D with [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) and [SLEAP](https://github.com/talmolab/sleap) or marker-based (such as [Simi Motion](http://www.simi.com/en/products/movement-analysis/simi-motion-2d3d.html?type=rss%2F)) as well as marker-less methods for obtaining 3D coordinates. 
+- AutoGaitA simplifies, accelerates, and standardises gait analyses (as well as the analysis of other rhythmic behaviours) after body posture tracking in 2D with [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) and [SLEAP](https://github.com/talmolab/sleap) or marker-based as well as marker-less (such as [Simi Motion](http://www.simi.com/en/products/movement-analysis/simi-motion-2d3d.html?type=rss%2F)) methods for obtaining 3D coordinates. 
 - AutoGaitA's first-level tools provide a wide range of automated kinematic analyses for each input video and AutoGaitA Group allows the comparison of up to six groups. 
 - AutoGaitA enables comparisons to be made across experimental conditions, species, disease states or genotypes. 
 - Despite being developed with gait data, AutoGaitA can be utilised for the analysis of any motor behaviour.

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/batchrun_scripts/dlc_multirun.py

@@ -43,6 +43,7 @@ def dlc_multirun():
     cfg["analyse_average_x"] = True
     cfg["standardise_x_coordinates"] = True
     cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = ""
     cfg["results_dir"] = ""
     cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
     cfg["fore_joints"] = [

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/batchrun_scripts/dlc_singlerun.py

@@ -23,7 +23,7 @@ def dlc_singlerun():
     cfg = {}
     cfg["sampling_rate"] = 100  # base cfg
     cfg["subtract_beam"] = True
-    cfg["dont_show_plots"] = False
+    cfg["dont_show_plots"] = True
     cfg["convert_to_mm"] = True
     cfg["pixel_to_mm_ratio"] = 3.76
     cfg["x_sc_broken_threshold"] = 200  # optional cfg
@@ -44,6 +44,9 @@ def dlc_singlerun():
     cfg["analyse_average_x"] = True
     cfg["standardise_x_coordinates"] = True
     cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = (
+        "/Users/mahan/sciebo/PythonCode/gaita_repo/autogaita/resources/Coordinate Standardisation Table Template.xlsx"
+    )
     cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
     cfg["fore_joints"] = [
         "Front paw tao ",

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/batchrun_scripts/sleap_singlerun.py

@@ -49,6 +49,7 @@ def sleap_singlerun():
     cfg["analyse_average_x"] = False
     cfg["standardise_x_coordinates"] = False
     cfg["x_standardisation_joint"] = ["Midfoot"]
+    cfg["coordinate_standardisation_xls"] = ""
     cfg["hind_joints"] = ["Midfoot", "Ankle", "Knee", "Hip"]
     cfg["fore_joints"] = []
     cfg["beam_col_left"] = []  # list of len == 1

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/batchrun_scripts/universal3D_multirun.py

@@ -34,6 +34,7 @@ def universal3D_multirun():
     cfg["analyse_average_y"] = True
     cfg["standardise_y_coordinates"] = True
     cfg["y_standardisation_joint"] = ["Foot"]
+    cfg["coordinate_standardisation_xls"] = ""
     cfg["joints"] = ["Midfoot", "Ankle", "Knee", "Hip", "Pelvis", "Shoulder", "Neck"]
     cfg["angles"] = {
         "name": ["Ankle", "Knee"],

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/batchrun_scripts/universal3D_singlerun.py

@@ -33,6 +33,7 @@ def universal3D_singlerun():
     cfg["analyse_average_y"] = True
     cfg["standardise_y_coordinates"] = True
     cfg["y_standardisation_joint"] = ["Midfoot, left"]
+    cfg["coordinate_standardisation_xls"] = ""
     cfg["joints"] = [
         # "R1-ThCx",
         "Midfoot",

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/common2D/common2D_1_preparation.py

@@ -1,5 +1,8 @@
 # %% imports
-from autogaita.resources.utils import write_issues_to_textfile
+from autogaita.resources.utils import (
+    write_issues_to_textfile,
+    standardise_primary_joint_coordinates,
+)
 from autogaita.common2D.common2D_constants import FILE_ID_STRING_ADDITIONS
 import os
 import shutil
@@ -48,6 +51,7 @@ def some_prep(tracking_software, info, folderinfo, cfg):
     analyse_average_x = cfg["analyse_average_x"]
     standardise_x_coordinates = cfg["standardise_x_coordinates"]
     standardise_y_to_a_joint = cfg["standardise_y_to_a_joint"]
+    coordinate_standardisation_xls = cfg["coordinate_standardisation_xls"]
 
     # .............................  move data  ........................................
     # => slightly different for DLC or SLEAP (see local functions below)
@@ -198,6 +202,7 @@ def some_prep(tracking_software, info, folderinfo, cfg):
         "x_standardisation_joint": x_standardisation_joint,
         "standardise_y_to_a_joint": standardise_y_to_a_joint,
         "y_standardisation_joint": y_standardisation_joint,
+        "coordinate_standardisation_xls": coordinate_standardisation_xls,
         "hind_joints": hind_joints,
         "fore_joints": fore_joints,
         "angles": angles,
@@ -236,7 +241,7 @@ def some_prep(tracking_software, info, folderinfo, cfg):
         )
         print(cols_are_weird_message)
         write_issues_to_textfile(cols_are_weird_message, info)
-    # if wanted: fix that deeplabcut inverses y
+    # if wanted: fix that deeplabcut & SLEAP inverse y
     if invert_y_axis:
         for col in data.columns:
             if col.endswith(" y"):
@@ -250,11 +255,6 @@ def some_prep(tracking_software, info, folderinfo, cfg):
         else:
             y_min = data[y_cols].min().min()
         data[y_cols] -= y_min
-    # convert pixels to millimeters
-    if convert_to_mm:
-        for column in data.columns:
-            if not column.endswith("likelihood"):
-                data[column] = data[column] / pixel_to_mm_ratio
     # quick warning if cfg is set to not flip gait direction but to standardise x
     if not flip_gait_direction and standardise_x_coordinates:
         message = (
@@ -295,6 +295,25 @@ def some_prep(tracking_software, info, folderinfo, cfg):
     # reorder the columns we added
     cols = [TIME_COL, "Flipped"]
     data = data[cols + [c for c in data.columns if c not in cols]]
+    # ------------------------------------------------------------------------
+    #                             IMPORTANT
+    # Next two things must be the last that are done in this function, since
+    # joint-standardisation must be done after beam-subtraction & non-beam-height-stand
+    # and pixel-standardisation must be done after joint-standardisation!
+    # ------------------------------------------------------------------------
+    # 1) standardise all primary joint (!) coordinates
+    # => all dimensions are divided by a fixed user-provided value
+    # => note this function has proper errors raised if things should be wrongly
+    #    configured by user!
+    if len(coordinate_standardisation_xls) > 0:
+        data, cfg = standardise_primary_joint_coordinates(
+            data, tracking_software, info, cfg
+        )
+    # 2) convert pixels to millimeters
+    if convert_to_mm:
+        for column in data.columns:
+            if column.endswith((" x", " y")):  # if tuple: endswith any of these
+                data[column] = data[column] / pixel_to_mm_ratio
     return data
 
 

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/common2D/common2D_2_sc_extraction.py

@@ -4,7 +4,8 @@ from autogaita.common2D.common2D_utils import (
     check_cycle_out_of_bounds,
     check_cycle_duplicates,
     check_cycle_order,
-    check_tracking,
+    check_tracking_xy_thresholds,
+    check_tracking_SLEAP_nans,
     handle_issues,
 )
 import os
@@ -23,7 +24,7 @@ from autogaita.common2D.common2D_constants import (
 # %% workflow step #2 - SC extraction (reading user-provided SC Table)
 
 
-def extract_stepcycles(data, info, folderinfo, cfg):
+def extract_stepcycles(tracking_software, data, info, folderinfo, cfg):
     """Read XLS file with SC annotations, find correct row & return all_cycles"""
 
     # ...............................  preparation  ....................................
@@ -212,6 +213,9 @@ def extract_stepcycles(data, info, folderinfo, cfg):
         all_cycles = check_cycle_duplicates(all_cycles)
         # check if user input progressively later latencies
         all_cycles = check_cycle_order(all_cycles, info)
-        # check if tracking broke for any SCs - if so remove them
-        all_cycles = check_tracking(data, info, all_cycles, cfg)
+        # check if tracking broke for any SCs using user-provided x and y thresholds
+        all_cycles = check_tracking_xy_thresholds(data, info, all_cycles, cfg)
+        # for SLEAP - check if there were any NaNs in any joints/angle-joints in SCs
+        if tracking_software == "SLEAP":
+            all_cycles = check_tracking_SLEAP_nans(data, info, all_cycles, cfg)
     return all_cycles

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/common2D/common2D_utils.py

@@ -210,7 +210,7 @@ def check_cycle_order(all_cycles, info):
     return clean_cycles
 
 
-def check_tracking(data, info, all_cycles, cfg):
+def check_tracking_xy_thresholds(data, info, all_cycles, cfg):
     """Check if any x/y column of any joint has broken datapoints"""
     # unpack
     convert_to_mm = cfg["convert_to_mm"]
@@ -241,7 +241,49 @@ def check_tracking(data, info, all_cycles, cfg):
                     exclude_this_cycle = True
         if exclude_this_cycle == True:
             this_message = (
-                "\n...excluding SC #" + str(c + 1) + " - DLC tracking failed!"
+                "\n...excluding SC #"
+                + str(c + 1)
+                + " - Tracking failed (coordinate-jump larger than x/y threshold)!"
+            )
+            print(this_message)
+            write_issues_to_textfile(this_message, info)
+        else:
+            if clean_cycles == None:
+                clean_cycles = [cycle]  # also makes a 2xscs list of lists
+            else:
+                clean_cycles.append(cycle)
+    return clean_cycles
+
+
+def check_tracking_SLEAP_nans(data, info, all_cycles, cfg):
+    """In SLEAP if tracking fails it generates NaNs - make sure we don't have those in any SC in any joint or angle-joint"""
+    # unpack
+    hind_joints = cfg["hind_joints"]
+    angles = cfg["angles"]
+    # all joints to test for NaNs
+    all_joints = hind_joints
+    for key in angles.keys():
+        all_joints += angles[key]
+    # columns to check
+    columns = []
+    for joint in all_joints:
+        columns.append(joint + "x")
+        columns.append(joint + "y")
+    # check for NaNs
+    clean_cycles = None
+    for c, cycle in enumerate(all_cycles):
+        exclude_this_cycle = False  # reset
+        for col in columns:
+            this_data = data.loc[cycle[0] : cycle[1], col]
+            if any(this_data.isna()):
+                exclude_this_cycle = True
+                NaN_joint = col
+                break
+        if exclude_this_cycle == True:
+            this_message = (
+                "\n...excluding SC #"
+                + str(c + 1)
+                + f" - Tracking failed (NaN found at {NaN_joint})!"
             )
             print(this_message)
             write_issues_to_textfile(this_message, info)

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/dlc/dlc_main.py

@@ -47,7 +47,7 @@ def dlc(info, folderinfo, cfg):
         return
 
     # .........................  step-cycle extraction  ................................
-    all_cycles = extract_stepcycles(data, info, folderinfo, cfg)
+    all_cycles = extract_stepcycles(tracking_software, data, info, folderinfo, cfg)
     if all_cycles is None:
         handle_issues("scs_invalid", info)
         if cfg["dont_show_plots"] is False:  # otherwise stuck at loading

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/common2D_advanced_config_gui.py

@@ -203,6 +203,19 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         )
         invert_y_axis_box.grid(row=12, column=0, columnspan=2)
 
+    # Standardise all (primary) joint coordinates by a fixed decimal value
+    coordinate_standardisation_xls_label, coordinate_standardisation_xls_entry = (
+        gaita_widgets.label_and_entry_pair(
+            cfg_window,
+            "Excel file for primary-joint coordinate standardisation:",
+            cfg["coordinate_standardisation_xls"],
+            widget_cfg,
+            adv_cfg_textsize=True,
+        )
+    )
+    coordinate_standardisation_xls_label.grid(row=13, column=0, columnspan=2)
+    coordinate_standardisation_xls_entry.grid(row=14, column=0, columnspan=2)
+
     #  .............................  advanced output  .................................
     # advanced analysis header
     adv_cfg_output_header_label = gaita_widgets.header_label(
@@ -211,7 +224,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         widget_cfg,
     )
     adv_cfg_output_header_label.grid(
-        row=13, column=0, rowspan=2, columnspan=2, sticky="nsew"
+        row=15, column=0, rowspan=2, columnspan=2, sticky="nsew"
     )
 
     # number of hindlimb (primary) joints to plot
@@ -222,8 +235,8 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         widget_cfg,
         adv_cfg_textsize=True,
     )
-    plot_joint_num__label.grid(row=15, column=0, columnspan=2)
-    plot_joint_num_entry.grid(row=16, column=0, columnspan=2)
+    plot_joint_num__label.grid(row=17, column=0, columnspan=2)
+    plot_joint_num_entry.grid(row=18, column=0, columnspan=2)
 
     # save to xls
     save_to_xls_box = gaita_widgets.checkbox(
@@ -233,7 +246,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         widget_cfg,
         adv_cfg_textsize=True,
     )
-    save_to_xls_box.grid(row=17, column=0, columnspan=2)
+    save_to_xls_box.grid(row=19, column=0, columnspan=2)
 
     # plot SE
     plot_SE_box = gaita_widgets.checkbox(
@@ -243,7 +256,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         widget_cfg,
         adv_cfg_textsize=True,
     )
-    plot_SE_box.grid(row=18, column=0, columnspan=2)
+    plot_SE_box.grid(row=20, column=0, columnspan=2)
 
     # color palette
     color_palette_string = "Choose figures' color palette"
@@ -252,7 +265,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         text=color_palette_string,
         font=(TEXT_FONT_NAME, ADV_CFG_TEXT_FONT_SIZE),
     )
-    color_palette_label.grid(row=19, column=0, columnspan=2)
+    color_palette_label.grid(row=21, column=0, columnspan=2)
     color_palette_entry = ctk.CTkOptionMenu(
         cfg_window,
         values=COLOR_PALETTES_LIST,
@@ -262,7 +275,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         button_hover_color=HOVER_COLOR,
         font=(TEXT_FONT_NAME, ADV_CFG_TEXT_FONT_SIZE),
     )
-    color_palette_entry.grid(row=20, column=0, columnspan=2)
+    color_palette_entry.grid(row=22, column=0, columnspan=2)
 
     # legend outside
     legend_outside_checkbox = gaita_widgets.checkbox(
@@ -272,18 +285,18 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         widget_cfg,
         adv_cfg_textsize=True,
     )
-    legend_outside_checkbox.grid(row=21, column=0, columnspan=2)
+    legend_outside_checkbox.grid(row=23, column=0, columnspan=2)
 
     # results dir
     results_dir_label, results_dir_entry = gaita_widgets.label_and_entry_pair(
         cfg_window,
-        "Save Results subfolders to directory below instead of to data's",
+        "Save Results subfolders to directory below instead of to data's:",
         cfg["results_dir"],
         widget_cfg,
         adv_cfg_textsize=True,
     )
-    results_dir_label.grid(row=22, column=0, columnspan=2)
-    results_dir_entry.grid(row=23, column=0, columnspan=2)
+    results_dir_label.grid(row=24, column=0, columnspan=2)
+    results_dir_entry.grid(row=25, column=0, columnspan=2)
 
     # done button
     adv_cfg_done_button = ctk.CTkButton(
@@ -295,7 +308,7 @@ def build_cfg_window(root, cfg, widget_cfg, root_dimensions):
         command=lambda: cfg_window.destroy(),
     )
     adv_cfg_done_button.grid(
-        row=24, column=0, columnspan=2, rowspan=2, sticky="nsew", padx=10, pady=(10, 5)
+        row=26, column=0, columnspan=2, rowspan=2, sticky="nsew", padx=10, pady=(10, 5)
     )
     # maximise widgets
     cfg_window.columnconfigure(list(range(2)), weight=1, uniform="Silent_Creme")

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/common2D_gui_constants.py

@@ -56,6 +56,7 @@ TK_STR_VARS = [
     "plot_joint_number",
     "color_palette",
     "results_dir",
+    "coordinate_standardisation_xls",
 ]
 GUI_SPECIFIC_VARS = {
     "FLOAT_VARS": FLOAT_VARS,

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/dlc_gui_config.json

@@ -40,6 +40,7 @@
         "color_palette": "Set2",
         "legend_outside": true,
         "results_dir": "",
+        "coordinate_standardisation_xls": "",
         "hind_joints": [
             "Hind paw tao",
             "Ankle",

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/gui_utils.py

@@ -43,9 +43,9 @@ def maximise_widgets(window):
 # ..............................  change widget states  ................................
 
 
-def change_widget_state_based_on_checkbox(cfg, key_of_checkbox, entry_to_change):
-    """Change the state of an entry widget based on whether a checkbox is checked."""
-    if cfg[key_of_checkbox].get() is True:
-        entry_to_change.configure(state="normal")
-    elif cfg[key_of_checkbox].get() is False:
-        entry_to_change.configure(state="disabled")
+def change_widget_state_based_on_checkbox(cfg, key_to_check, widget_to_change):
+    """Change the state of a widget based on state of another widget."""
+    if cfg[key_to_check].get() is True:
+        widget_to_change.configure(state="normal")
+    elif cfg[key_to_check].get() is False:
+        widget_to_change.configure(state="disabled")

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/sleap_gui_config.json

@@ -40,6 +40,7 @@
         "color_palette": "Set2",
         "legend_outside": true,
         "results_dir": "",
+        "coordinate_standardisation_xls": "",
         "hind_joints": [
             "Midfoot",
             "Ankle",

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/universal3D_gui.py

@@ -71,6 +71,7 @@ TK_STR_VARS = [
     "sctable_filename",
     "postname_string",
     "color_palette",
+    "coordinate_standardisation_xls",
     "fileprep_root_dir",  # for datafile prep window only
     "fileprep_filetype",
     "fileprep_postname_string",
@@ -696,6 +697,18 @@ def build_cfg_window(root, cfg):
     gui_utils.change_widget_state_based_on_checkbox(
         cfg, "standardise_y_coordinates", y_standardisation_joint_entry
     )
+    # standardise all (primary) joint coordinates by a fixed decimal value
+    coordinate_standardisation_xls_label, coordinate_standardisation_xls_entry = (
+        gaita_widgets.label_and_entry_pair(
+            cfg_window,
+            "Excel file for primary-joint coordinate standardisation:",
+            cfg["coordinate_standardisation_xls"],
+            WIDGET_CFG,
+            adv_cfg_textsize=True,
+        )
+    )
+    coordinate_standardisation_xls_label.grid(row=12, column=0, columnspan=2)
+    coordinate_standardisation_xls_entry.grid(row=13, column=0, columnspan=2)
 
     #  .............................  advanced output  .................................
     # advanced output header
@@ -703,7 +716,7 @@ def build_cfg_window(root, cfg):
         cfg_window, "Output", WIDGET_CFG
     )
     adv_cfg_output_header_label.grid(
-        row=12, column=0, rowspan=2, columnspan=2, sticky="nsew"
+        row=14, column=0, rowspan=2, columnspan=2, sticky="nsew"
     )
     # number of joints to plot
     plot_joint_num_label, plot_joint_num_entry = gaita_widgets.label_and_entry_pair(
@@ -713,8 +726,8 @@ 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=16, column=0, sticky="e")
+    plot_joint_num_entry.grid(row=16, column=1, sticky="w")
     # plot plots to python
     showplots_checkbox = gaita_widgets.checkbox(
         cfg_window,
@@ -723,7 +736,7 @@ 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=17, column=0, columnspan=2)
     # plot SE
     plot_SE_box = gaita_widgets.checkbox(
         cfg_window,
@@ -732,7 +745,7 @@ 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=18, column=0, columnspan=2)
     # color palette
     color_palette_string = "Choose figures' color palette"
     color_palette_label = ctk.CTkLabel(
@@ -740,7 +753,7 @@ 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=19, column=0, columnspan=2)
     color_palette_entry = ctk.CTkOptionMenu(
         cfg_window,
         values=COLOR_PALETTES_LIST,
@@ -750,7 +763,7 @@ 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=20, column=0, columnspan=2)
     # legend outside
     legend_outside_checkbox = gaita_widgets.checkbox(
         cfg_window,
@@ -759,7 +772,7 @@ 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=21, column=0, columnspan=2)
 
     # results dir
     results_dir_label, results_dir_entry = gaita_widgets.label_and_entry_pair(
@@ -769,8 +782,8 @@ 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=22, column=0, columnspan=2)
+    results_dir_entry.grid(row=23, column=0, columnspan=2)
 
     # done button
     adv_cfg_done_button = ctk.CTkButton(
@@ -782,7 +795,7 @@ 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=24, column=0, rowspan=2, columnspan=2, sticky="nsew", padx=10, pady=(10, 5)
     )
     # maximise widgets
     cfg_window.columnconfigure(list(range(2)), weight=1, uniform="Silent_Creme")

{autogaita-1.1.0 → autogaita-1.1.1}/autogaita/gui/universal3D_gui_config.json

@@ -29,6 +29,7 @@
         "color_palette": "Set2",
         "legend_outside": true,
         "results_dir": "",
+        "coordinate_standardisation_xls": "",
         "joints": [
             "Midfoot",
             "Ankle ",