autogaita 1.0.6__tar.gz → 1.0.8__tar.gz

{autogaita-1.0.6 → autogaita-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.6
+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-1.0.6 → autogaita-1.0.8}/autogaita/batchrun_scripts/group_dlcrun.py

@@ -42,20 +42,17 @@ def group_dlcrun():
         "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/25mm/Results/",
     ]
     folderinfo["results_dir"] = (
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results5/"
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
         # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Mahan Results/"
         # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/GroupResults/"
     )
-    folderinfo["load_dir"] = (
-        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/example_data_results/"
-        # ""
-    )
+    folderinfo["load_dir"] = ""
     # cfg
     cfg = {}
-    cfg["do_permtest"] = True
+    cfg["do_permtest"] = False  # True
     cfg["do_anova"] = True
     cfg["permutation_number"] = 100
-    cfg["PCA_n_components"] = 3
+    cfg["PCA_n_components"] = 6
     # cfg["PCA_n_components"] = 0.33
     # cfg["PCA_custom_scatter_PCs"] = "4,5,6;4,5;2,4,6"
     cfg["PCA_custom_scatter_PCs"] = ""
@@ -71,23 +68,7 @@ def group_dlcrun():
     # cfg["anova_design"] = "Mixed ANOVA"
     cfg["permutation_number"] = 100
     cfg["PCA_variables"] = [
-        "Hind paw tao y",
-        "Ankle y",
-        "Knee y",
-        "Ankle Angle",
-        "Knee Angle",
-        "Nose x",
-        "Knee y",
-        "Knee x",
-        "Knee Velocity",
-        "Knee Acceleration",
-        "Knee Angle",
-        "Knee Angle Velocity",
-        "Knee Angle Acceleration",
-        "Hip Angle",
-    ]
-    cfg["stats_variables"] = [
-        "Hind paw tao y",
+        # "Hind paw tao y",
         # "Ankle y",
         # "Knee y",
         # "Ankle Angle",
@@ -101,6 +82,22 @@ def group_dlcrun():
         # "Knee Angle Velocity",
         # "Knee Angle Acceleration",
         # "Hip Angle",
+    ]
+    cfg["stats_variables"] = [
+        "Hind paw tao y",
+        # "Ankle y",
+        "Knee y",
+        # "Ankle Angle",
+        "Knee Angle",
+        # "Nose x",
+        # "Knee y",
+        "Knee x",
+        # "Knee Velocity",
+        # "Knee Acceleration",
+        # "Knee Angle",
+        # "Knee Angle Velocity",
+        # "Knee Angle Acceleration",
+        # "Hip Angle",
         # "Elbow Angle"
     ]
     # run

autogaita-1.0.6/autogaita/batchrun_scripts/group_universal3Drun_backup.py → autogaita-1.0.8/autogaita/batchrun_scripts/group_universal3Drun.py

@@ -29,8 +29,6 @@ def group_universal3Drun():
         cfg["do_anova"] = True
         cfg["permutation_number"] = 10
         cfg["PCA_n_components"] = 3
-        cfg["PCA_custom_scatter_PCs"] = ""
-        cfg["PCA_bins"] = ""
         cfg["PCA_save_3D_video"] = False
         cfg["stats_threshold"] = 0.05
         cfg["plot_SE"] = False

{autogaita-1.0.6 → 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-1.0.6 → 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-1.0.6 → autogaita-1.0.8}/autogaita/common2D/common2D_3_analysis.py

@@ -63,9 +63,6 @@ def analyse_and_export_stepcycles(data, all_cycles, info, cfg):
     # 2 or more steps - build dataframe
     elif len(all_cycles) > 1:
         # first- step is added manually
-        # NOTE
-        # ----
-        # normalised_steps_data is created using x_standardised_steps_data or first_step
         first_step = data_copy.loc[all_cycles[0][0] : all_cycles[0][1]]
         if standardise_x_coordinates:
             all_steps_data, x_standardised_steps_data = (
@@ -184,20 +181,20 @@ def standardise_x_y_and_add_features_to_one_step(step, cfg):
         step_copy[y_cols] -= this_y_min
     # if no x-standardisation, just add features & return non-(x-)normalised step
     if cfg["standardise_x_coordinates"] is False:
-        non_stand_step = add_features(step_copy, cfg)
-        return non_stand_step
+        non_norm_step = add_features(step_copy, cfg)
+        return non_norm_step
         # else standardise x (horizontal dimension) at step-cycle level too
     else:
-        non_stand_step = add_features(step_copy, cfg)
-        x_stand_step = step_copy.copy()
-        x_cols = [col for col in x_stand_step.columns if col.endswith("x")]
+        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!!
-        min_x_standardisation_joint = x_stand_step[
+        min_x_standardisation_joint = x_norm_step[
             cfg["x_standardisation_joint"][0] + "x"
         ].min()
-        x_stand_step[x_cols] -= min_x_standardisation_joint
-        x_stand_step = add_features(x_stand_step, cfg)
-        return non_stand_step, x_stand_step
+        x_norm_step[x_cols] -= min_x_standardisation_joint
+        x_norm_step = add_features(x_norm_step, cfg)
+        return non_norm_step, x_norm_step
 
 
 def add_features(step, cfg):

{autogaita-1.0.6 → 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-1.0.6 → autogaita-1.0.8}/autogaita/group/group_3_PCA.py

@@ -218,8 +218,6 @@ def run_PCA(PCA_df, features, cfg):
     # excel files)
     x = pd.DataFrame(x, columns=features)
     # NOTE that this next line changes the PCA_model variable!
-    # pdb.set_trace()
-    x.fillna(0, inplace=True)
     PCs = PCA_model.fit_transform(x)
     # NOTE! we use number_of_PCs from here onwards (in info/plots/etc) to differentiate
     #       between n_components which can be smaller than 1!

{autogaita-1.0.6 → 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-1.0.6 → 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/group_gui_config.json

@@ -0,0 +1,42 @@
+[
+    {
+        "group_names": [
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "group_dirs": [
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
+        ],
+        "results_dir": "",
+        "load_dir": ""
+    },
+    {
+        "do_permtest": true,
+        "do_anova": false,
+        "anova_design": "RM ANOVA",
+        "permutation_number": "10000",
+        "stats_threshold": "0.05",
+        "which_leg": "right",
+        "PCA_n_components": "3",
+        "PCA_custom_scatter_PCs": "",
+        "PCA_save_3D_video": false,
+        "PCA_bins": "",
+        "plot_SE": false,
+        "color_palette": "Set2",
+        "dont_show_plots": false,
+        "legend_outside": true,
+        "stats_variables": [
+        ],
+        "PCA_variables": [
+        ]
+    }
+]

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-1.0.6 → 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