autogaita 1.0.2__tar.gz → 1.0.3__tar.gz

{autogaita-1.0.2 → autogaita-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.2
+Version: 1.0.3
 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-1.0.3/autogaita/batchrun_scripts/group_dlcrun.py

@@ -0,0 +1,206 @@
+import autogaita
+
+
+def group_dlcrun():
+    """
+    Batchrun script to run AutoGaitA Group for Results obtained with AutoGaitA DLC.
+    folderinfo & cfg dictionaries must be configured as explained in our documentation. See the "AutoGaitA without the GUI" section of our documentation for references to in-depth explanations to all dictionary keys (note that each key of dicts corresponds to some object in the AutoGaitA Group GUI)
+    """
+    # folderinfo
+    # => Note that length of folderinfo's group_names & group_dirs lists determines how #    many groups are compared.
+    # => Also note that indices must correspond (i.e., idx #    1's name will be used #    for dataset stored in group_dir's idx 1)
+    folderinfo = {}
+    folderinfo["group_names"] = [
+        # ----------
+        # RM Dataset
+        # "5mm",
+        # "12mm",
+        # "25mm",
+        # -------
+        # Interaction Issue Dataset
+        # "Control",
+        # "Silenced",
+        # --------
+        # Testing Dataset
+        # "one",
+        # "two",
+        # --------
+        # Beam x Age for Manuscript
+        "3m_5mm",
+        "3m_12mm",
+        "3m_25mm",
+        "24m_5mm",
+        "24m_12mm",
+        "24m_25mm",
+    ]
+    folderinfo["group_dirs"] = [
+        # --------------------------
+        # Full Dataset (39 subjects)
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control Full",
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced Full/",
+        # --------------------------
+        # Reduced Dataset (5 subjects)
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control",
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced/",
+        # --------------------------
+        # Testing Dataset
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 1/",
+        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 2/",
+        # --------------------------
+        # RM Dataset (example data in repo)
+        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/5mm/Results/",
+        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/12mm/Results/",
+        # "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/25mm/Results/",
+        # --------------------------
+        # Beam x Age for Manuscript
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/9w",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/9w",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/25mm/9w",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/104w",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/104w",
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/25mm/104w"
+    ]
+    folderinfo["results_dir"] = (
+        # "/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/"
+        "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/YoungOld3BeamsForPaper"
+    )
+    # cfg
+    cfg = {}
+    cfg["do_permtest"] = False  # True
+    cfg["do_anova"] = True
+    cfg["permutation_number"] = 100
+    cfg["PCA_n_components"] = 0.9
+    cfg["PCA_custom_scatter_PCs"] = "1,3;2,3;2,3,4;;;;"
+    cfg["PCA_save_3D_video"] = False
+    cfg["PCA_bins"] = ""  # "0-10,24,50-75"
+    cfg["stats_threshold"] = 0.05
+    cfg["plot_SE"] = True
+    cfg["color_palette"] = "inferno"
+    cfg["dont_show_plots"] = True
+    cfg["legend_outside"] = True
+    cfg["which_leg"] = "left"
+    cfg["anova_design"] = "RM ANOVA"
+    # cfg["anova_design"] = "Mixed ANOVA"
+    cfg["PCA_variables"] = [
+        # Beam x Age
+        "Nose x",
+        "Nose y",
+        "Ear base x",
+        "Ear base y",
+        "Front paw tao x",
+        "Front paw tao y",
+        "Wrist x",
+        "Wrist y",
+        "Elbow x",
+        "Elbow y",
+        "Lower Shoulder x",
+        "Lower Shoulder y",
+        "Upper Shoulder x",
+        "Upper Shoulder y",
+        "Iliac Crest x",
+        "Iliac Crest y",
+        "Hip x",
+        "Hip y",
+        "Knee x",
+        "Knee y",
+        "Ankle x",
+        "Ankle y",
+        "Hind paw tao x",
+        "Hind paw tao y",
+        "Tail base y",
+        "Tail center x",
+        "Tail center y",
+        "Tail tip x",
+        "Tail tip y",
+        "Hind paw tao Velocity",
+        "Hind paw tao Acceleration",
+        "Ankle Velocity",
+        "Ankle Acceleration",
+        "Knee Velocity",
+        "Knee Acceleration",
+        "Hip Velocity",
+        "Hip Acceleration",
+        "Iliac Crest Velocity",
+        "Iliac Crest Acceleration",
+        "Ankle Angle",
+        "Knee Angle",
+        "Hip Angle",
+        "Wrist Angle",
+        "Elbow Angle",
+        "Lower Shoulder Angle",
+        "Iliac Crest Angle",
+        "Ankle Angle Velocity",
+        "Ankle Angle Acceleration",
+        "Knee Angle Acceleration",
+        "Hip Angle Velocity",
+        "Hip Angle Acceleration",
+        "Wrist Angle Velocity",
+        "Wrist Angle Acceleration",
+        "Elbow Angle Velocity",
+        "Elbow Angle Acceleration",
+        "Lower Shoulder Angle Velocity",
+        "Lower Shoulder Angle Acceleration",
+        "Iliac Crest Angle Velocity",
+        "Iliac Crest Angle Acceleration",
+
+
+        # PREVIOUS TESTING FEATURES
+        # -----------------
+        # "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",
+        # "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"
+
+
+        # Beam x Age
+        "Hip x",
+        "Hip y",
+        "Knee x",
+        "Knee y",
+        "Ankle x",
+        "Ankle y",
+        "Hind paw tao x",
+        "Hind paw tao y",
+        "Hind paw tao Velocity",
+        "Ankle Velocity",
+        "Knee Velocity",
+        "Ankle Angle",
+        "Knee Angle",
+        "Hip Angle"
+    ]
+    # run
+    autogaita.group(folderinfo, cfg)
+
+
+# %% what happens if we just hit run
+if __name__ == "__main__":
+    group_dlcrun()

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_1_preparation.py

@@ -1,8 +1,7 @@
 # %% imports
-from autogaita.group.group_utils import write_issues_to_textfile
+from autogaita.resources.utils import write_issues_to_textfile
 import os
 import json
-import numpy as np
 import matplotlib.pyplot as plt
 import seaborn as sns
 
@@ -110,7 +109,6 @@ def extract_cfg_vars(folderinfo, cfg):
 
     group_names = folderinfo["group_names"]
     group_dirs = folderinfo["group_dirs"]
-    results_dir = folderinfo["results_dir"]
 
     # ................................  save_to_xls  ...................................
     save_to_xls = [None] * len(group_dirs)
@@ -143,7 +141,7 @@ def extract_cfg_vars(folderinfo, cfg):
                     save_to_xls[g] = False
                 if save_to_xls[g] is True:
                     print(sheet_type_mismatch_message)
-                    write_issues_to_textfile(sheet_type_mismatch_message, results_dir)
+                    write_issues_to_textfile(sheet_type_mismatch_message, folderinfo)
             # case 2: we found a xlsx file
             elif os.path.exists(
                 os.path.join(
@@ -158,7 +156,7 @@ def extract_cfg_vars(folderinfo, cfg):
                 if save_to_xls[g] is False:
                     save_to_xls[g] = True
                     print(sheet_type_mismatch_message)
-                    write_issues_to_textfile(sheet_type_mismatch_message, results_dir)
+                    write_issues_to_textfile(sheet_type_mismatch_message, folderinfo)
         # test that at least 1 folder has valid results for all groups
         if not valid_results_folders:
             no_valid_results_error = (
@@ -168,7 +166,7 @@ def extract_cfg_vars(folderinfo, cfg):
                 + "\nFix & re-run!"
             )
             print(no_valid_results_error)
-            write_issues_to_textfile(no_valid_results_error, results_dir)
+            write_issues_to_textfile(no_valid_results_error, folderinfo)
     # assign to our cfg dict after group loop
     cfg["save_to_xls"] = save_to_xls
 
@@ -190,7 +188,7 @@ def extract_cfg_vars(folderinfo, cfg):
                 + str(cfg["PCA_n_components"])
                 + "\n Fix & re-run!"
             )
-            write_issues_to_textfile(PCA_error_message, results_dir)
+            write_issues_to_textfile(PCA_error_message, folderinfo)
             raise ValueError(PCA_error_message)
         if cfg["PCA_n_components"] < 2:
             print(
@@ -217,7 +215,7 @@ def extract_cfg_vars(folderinfo, cfg):
             + "\n".join(list(set(duplicate_vars)))
         )
         print(PCA_duplicates_error_message)
-        write_issues_to_textfile(PCA_duplicates_error_message, results_dir)
+        write_issues_to_textfile(PCA_duplicates_error_message, folderinfo)
         cfg["PCA_variables"] = unique_PCA_vars
     # check if PCA bin num is valid, two tests and 1 fix
     # => note there is separate code that transforms this string input into an int-list
@@ -249,7 +247,7 @@ def extract_cfg_vars(folderinfo, cfg):
         #    so we just stop everything and help them fix it
         if PCA_bins_error_message:
             print(PCA_bins_error_message)
-            write_issues_to_textfile(PCA_bins_error_message, results_dir)
+            write_issues_to_textfile(PCA_bins_error_message, folderinfo)
             raise ValueError(PCA_bins_error_message)
         # fix for users: remove first and last characters if not digits
         while not cfg["PCA_bins"][0].isdigit():

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_2_data_processing.py

@@ -1,6 +1,5 @@
 # %% imports
-from autogaita.resources.utils import bin_num_to_percentages
-from autogaita.group.group_utils import write_issues_to_textfile
+from autogaita.resources.utils import bin_num_to_percentages, write_issues_to_textfile
 import os
 import pandas as pd
 import numpy as np
@@ -95,7 +94,7 @@ def import_data(folderinfo, cfg):
                     tracking_software,
                     name,
                     which_leg,
-                    results_dir,
+                    folderinfo,
                     cfg,
                 )
             df_dict[which_df][g] = final_df_checks_and_save_to_xls(
@@ -109,7 +108,7 @@ def import_data(folderinfo, cfg):
     # test: is bin_num is consistent across our groups
     # => if so, add it as well as one_bin_in_% to cfg
     cfg["bin_num"] = test_bin_num_consistency(
-        df_dict["Normalised"], group_names, results_dir
+        df_dict["Normalised"], group_names, folderinfo
     )
     dfs = df_dict["Normalised"]
     raw_dfs = df_dict["Original"]
@@ -147,7 +146,7 @@ def final_df_checks_and_save_to_xls(
     return this_df
 
 
-def test_bin_num_consistency(dfs, group_names, results_dir):
+def test_bin_num_consistency(dfs, group_names, folderinfo):
     """Tests if bin number of step-cycle normalisation is consistent across groups"""
     # For this we use sc_breaks [i.e. the nan step-separators]) to see if bin_num is the
     # same value across all individual step-cycles across all groups.
@@ -166,17 +165,15 @@ def test_bin_num_consistency(dfs, group_names, results_dir):
             this_bin_num = sc_breaks[b] - sc_breaks[b - 1] - 1
             if this_bin_num != bin_num:
                 bin_num_error_helper_function(
-                    dfs, g, group_names, sc_breaks, results_dir, b
+                    folderinfo, dfs, g, group_names, sc_breaks, b
                 )
         # handle the last step-cycle of the df (it doesn't have a sc_break after it!)
         if (len(dfs[g]) - sc_breaks[-1] - 1) != this_bin_num:
-            bin_num_error_helper_function(
-                dfs, g, group_names, sc_breaks, results_dir, b
-            )
+            bin_num_error_helper_function(folderinfo, dfs, g, group_names, sc_breaks, b)
     return bin_num
 
 
-def bin_num_error_helper_function(dfs, g, group_names, sc_breaks, results_dir, b):
+def bin_num_error_helper_function(folderinfo, dfs, g, group_names, sc_breaks, b):
     """Handle this error in a separate function for readability"""
     id_col_idx = dfs[g].columns.get_loc(ID_COL)
     message = (
@@ -189,11 +186,11 @@ def bin_num_error_helper_function(dfs, g, group_names, sc_breaks, results_dir, b
         + "\nPlease re-run & make sure all bin numbers match!"
     )
     print(message)
-    write_issues_to_textfile(message, results_dir)
+    write_issues_to_textfile(message, folderinfo)
     raise ValueError(message)
 
 
-def test_PCA_and_stats_variables(df, group_name, name, results_dir, cfg):
+def test_PCA_and_stats_variables(df, group_name, name, folderinfo, cfg):
     """Tests if PCA & stats variables are present in all groups' datasets"""
     PCA_variables = cfg["PCA_variables"]
     stats_variables = cfg["stats_variables"]
@@ -215,7 +212,7 @@ def test_PCA_and_stats_variables(df, group_name, name, results_dir, cfg):
                 + "\nPlease re-run & make sure all variables are present!"
             )
             print(PCA_variable_mismatch_message)
-            write_issues_to_textfile(PCA_variable_mismatch_message, results_dir)
+            write_issues_to_textfile(PCA_variable_mismatch_message, folderinfo)
             raise ValueError(PCA_variable_mismatch_message)
     if stats_variables:
         if not all(variable in df.columns for variable in stats_variables):
@@ -235,7 +232,7 @@ def test_PCA_and_stats_variables(df, group_name, name, results_dir, cfg):
                 + "\nPlease re-run & make sure all variables are present!"
             )
             print(stats_variable_mismatch_message)
-            write_issues_to_textfile(stats_variable_mismatch_message, results_dir)
+            write_issues_to_textfile(stats_variable_mismatch_message, folderinfo)
             raise ValueError(stats_variable_mismatch_message)
 
 
@@ -247,7 +244,7 @@ def import_and_combine_dfs(
     tracking_software,
     name,
     which_leg,
-    results_dir,
+    folderinfo,
     cfg,
 ):
     """Import one run's df at a time and combine to group-level df"""
@@ -274,11 +271,11 @@ def import_and_combine_dfs(
             + ".\nSkipping!"
         )
         print(this_message)
-        write_issues_to_textfile(this_message, results_dir)
+        write_issues_to_textfile(this_message, folderinfo)
     else:
         df_copy = df.copy()
         # test: are our PCA & stats variables present in this ID's dataset?
-        test_PCA_and_stats_variables(df_copy, group_name, name, results_dir, cfg)
+        test_PCA_and_stats_variables(df_copy, group_name, name, folderinfo, cfg)
         # add some final info & append to group_df
         if tracking_software == "DLC":
             # add this run's info to df (& prepare Stepcycle column)

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_3_PCA.py

@@ -1,6 +1,6 @@
 # %% imports
-from autogaita.resources.utils import bin_num_to_percentages
-from autogaita.group.group_utils import save_figures, write_issues_to_textfile
+from autogaita.resources.utils import bin_num_to_percentages, write_issues_to_textfile
+from autogaita.group.group_utils import save_figures
 import os
 import string
 import pandas as pd
@@ -33,7 +33,6 @@ def PCA_main(avg_dfs, folderinfo, cfg, plot_panel_instance):
     """PCA on features of interest"""
 
     # unpack
-    results_dir = folderinfo["results_dir"]
     PCA_custom_scatter_PCs = cfg["PCA_custom_scatter_PCs"]
     PCA_bins = cfg["PCA_bins"]
 
@@ -58,7 +57,7 @@ def PCA_main(avg_dfs, folderinfo, cfg, plot_panel_instance):
             + "var-explained approach!"
         )
         print(PCA_error_message_1)
-        write_issues_to_textfile(PCA_error_message_1, results_dir)
+        write_issues_to_textfile(PCA_error_message_1, folderinfo)
         return
     # plot barplot of cumulative explained variance
     plot_PCA_barplot(PCA_info, folderinfo, cfg, plot_panel_instance)
@@ -96,7 +95,6 @@ def convert_PCA_bins_to_list(folderinfo, cfg):
     for this
     """
     # unpack
-    results_dir = folderinfo["results_dir"]
     PCA_bins = cfg["PCA_bins"]
     bin_num = cfg["bin_num"]
 
@@ -121,7 +119,7 @@ def convert_PCA_bins_to_list(folderinfo, cfg):
                     + "\nPlease check your input and try again!"
                 )
                 print(PCA_bins_error_message)
-                write_issues_to_textfile(PCA_bins_error_message, results_dir)
+                write_issues_to_textfile(PCA_bins_error_message, folderinfo)
                 raise ValueError(PCA_bins_error_message)
 
         else:
@@ -143,7 +141,6 @@ def create_PCA_df(avg_dfs, folderinfo, cfg):
     """Create a ID x ID_COL + features dataframe to be used by PCA"""
 
     # unpack
-    results_dir = folderinfo["results_dir"]
     group_names = folderinfo["group_names"]
     PCA_vars = cfg["PCA_variables"]
     bin_num = cfg["bin_num"]
@@ -193,7 +190,7 @@ def create_PCA_df(avg_dfs, folderinfo, cfg):
             + "This should never happen, please contact me!"
         )
         print(critical_PCA_df_error_message)
-        write_issues_to_textfile(critical_PCA_df_error_message, results_dir)
+        write_issues_to_textfile(critical_PCA_df_error_message, folderinfo)
         raise ValueError(critical_PCA_df_error_message)
     # add colnames after the last mouse (makes concat'ing series 2 df easier)
     PCA_df.columns = [GROUP_COL] + [ID_COL] + features
@@ -259,7 +256,8 @@ def PCA_info_to_xlsx(PCA_df, PCA_info, folderinfo, cfg):
 
     # add column headers
     for pc in range(number_of_PCs):
-        sheet[string.ascii_uppercase[pc + 1] + "1"] = "PC " + str(pc + 1)
+        # pdb.set_trace()
+        sheet.cell(row=1, column=pc + 2, value="PC " + str(pc + 1))
     # add cell values: explained variance
     sheet.cell(row=2, column=1, value="Explained Var. (%)")
     for pc in range(number_of_PCs):
@@ -372,7 +370,7 @@ def plot_PCA_scatterplots(
                 + "!\nThe PC you wanted was not computed by PCA!"
             )
             print(invalid_custom_PC_scatter_message)
-            write_issues_to_textfile(invalid_custom_PC_scatter_message, results_dir)
+            write_issues_to_textfile(invalid_custom_PC_scatter_message, folderinfo)
             return
         # after the test we can overwrite "real" number of PCs of full PCA here since
         # we only use this value to know if we also do a 3D plot or not from here on

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_4_stats.py

@@ -1,11 +1,10 @@
 # %% imports
-from autogaita.resources.utils import bin_num_to_percentages
+from autogaita.resources.utils import bin_num_to_percentages, write_issues_to_textfile
 from autogaita.group.group_utils import (
     check_mouse_conversion,
     save_figures,
     ytickconvert_mm_to_cm,
     ylabel_velocity_and_acceleration,
-    write_issues_to_textfile,
 )
 import os
 import sys
@@ -16,7 +15,7 @@ import openpyxl
 from sklearn.utils import shuffle
 import matplotlib.pyplot as plt
 from scipy import stats
-import pingouin as pg
+import pingouin as pg  # important for ANOVAs!
 
 # %% constants
 from autogaita.resources.constants import INFO_TEXT_WIDTH, ID_COL, SC_PERCENTAGE_COL
@@ -489,11 +488,14 @@ def extract_all_clusters(trueobs_results_df, contrast):
 
 # ...............................  sanity check . ......................................
 def anova_design_sanity_check(stats_df, folderinfo, cfg):
-    """Sanity check the anova_design input of the user based on stats_df's IDs"""
+    """Sanity check the anova_design input of the user based on stats_df's IDs
+    Note
+    ----
+    This function also catches cases in which a user might have a 2-way design and just wants to run Tukeys (see below for 2-way #1 and #2)
+    """
 
     # unpack
     anova_design = cfg["anova_design"]
-    results_dir = folderinfo["results_dir"]
 
     # get IDs for each group to check if they are unique
     group_IDs = stats_df.groupby("Group")["ID"].unique()
@@ -508,7 +510,7 @@ def anova_design_sanity_check(stats_df, folderinfo, cfg):
     if anova_design == "Mixed ANOVA":
         if len(ID_list) == len(unique_ID_list):  # check passed
             return True
-        else:
+        else:  # 2-way #1 is caught here (non-unique IDs when Mixed)
             mixed_anova_error_message = (
                 "\n*********\n! ERROR !\n*********\n"
                 + "\nANOVA design seems wrong - skipping ANOVA!"
@@ -518,7 +520,7 @@ def anova_design_sanity_check(stats_df, folderinfo, cfg):
                 + str(group_IDs)
             )
             print(mixed_anova_error_message)
-            write_issues_to_textfile(mixed_anova_error_message, results_dir)
+            write_issues_to_textfile(mixed_anova_error_message, folderinfo)
             return False
     # RM ANOVA - IDs in each group must be the same!
     elif anova_design == "RM ANOVA":
@@ -539,9 +541,12 @@ def anova_design_sanity_check(stats_df, folderinfo, cfg):
                 + "analyses will be included in RM ANOVA:\n\n"
                 + str(valid_IDs)
             )
-            print(rm_anova_info_message)
-            write_issues_to_textfile(rm_anova_info_message, results_dir)
-            return True
+            if valid_IDs:
+                print(rm_anova_info_message)
+                write_issues_to_textfile(rm_anova_info_message, folderinfo)
+                return True
+            else:  # 2-way #2 here: not all IDs in all groups in a RM design
+                return False
         else:
             rm_anova_error_message = (
                 "\n*********\n! ERROR !\n*********\n"
@@ -552,13 +557,20 @@ def anova_design_sanity_check(stats_df, folderinfo, cfg):
                 + str(group_IDs)
             )
             print(rm_anova_error_message)
-            write_issues_to_textfile(rm_anova_error_message, results_dir)
+            write_issues_to_textfile(rm_anova_error_message, folderinfo)
             return False
 
 
 # ...............................  main function  ......................................
 def ANOVA_main(
-    stats_df, g_avg_dfs, g_std_dfs, stats_var, folderinfo, cfg, plot_panel_instance
+    stats_df,
+    g_avg_dfs,
+    g_std_dfs,
+    stats_var,
+    just_do_tukeys,
+    folderinfo,
+    cfg,
+    plot_panel_instance,
 ):
     """Perform a two-way RM-ANOVA with the factors group (between or within) & SC
     percentage (within) on a given dependent variable
@@ -570,9 +582,10 @@ def ANOVA_main(
     # initialise text file
     initial_stats_textfile(stats_var, anova_design, folderinfo)
 
-    # run the 1-way RM or Mixed ANOVA
+    # run the fully RM or Mixed ANOVA
     # => note pingouin checks both or sphericity by default
-    ANOVA_result = run_ANOVA(stats_df, stats_var, cfg)
+    if just_do_tukeys is False:
+        ANOVA_result = run_ANOVA(stats_df, stats_var, cfg)
 
     # run Tukeys for pairwise comparisons
     # => always running multiple comparison tests as well. see Prism's doc for why

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_main.py

@@ -13,7 +13,7 @@ from autogaita.group.group_4_stats import (
     ANOVA_main,
 )
 from autogaita.group.group_5_plots import plot_results
-from autogaita.group.group_utils import print_start
+from autogaita.group.group_utils import print_start, tukeys_only_info_message
 from autogaita.resources.utils import print_finish, PlotPanel
 import matplotlib
 import matplotlib.pyplot as plt
@@ -105,13 +105,18 @@ def group(folderinfo, cfg):
 
         # ..................................  ANOVA  ...................................
         if cfg["do_anova"]:  # indentation since we check for stats-vars here too!
-            if anova_design_sanity_check(stats_df, folderinfo, cfg):
+            if anova_design_sanity_check(stats_df, folderinfo, cfg) is not True:
+                just_do_tukeys = True
+                tukeys_only_info_message(folderinfo)
+            else:
+                just_do_tukeys = False
                 for stats_var in cfg["stats_variables"]:
                     ANOVA_main(
                         stats_df,
                         g_avg_dfs,
                         g_std_dfs,
                         stats_var,
+                        just_do_tukeys,
                         folderinfo,
                         cfg,
                         plot_panel_instance,

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita/group/group_utils.py

@@ -1,6 +1,6 @@
 import os
-
-from autogaita.resources.constants import ISSUES_TXT_FILENAME, INFO_TEXT_WIDTH
+from autogaita.resources.utils import write_issues_to_textfile
+from autogaita.resources.constants import INFO_TEXT_WIDTH
 from autogaita.group.group_constants import (
     GROUP_CONFIG_TXT_FILENAME,
     PCA_CUSTOM_SCATTER_OUTER_SEPARATOR,
@@ -63,6 +63,11 @@ def print_start(folderinfo, cfg):
             cfg["PCA_custom_scatter_PCs"] = cfg["PCA_custom_scatter_PCs"].replace(
                 " ", ""  # remove spaces for user if they included them (not allowed!)
             )
+            # string cannot end with the ; separator this will break later
+            while cfg["PCA_custom_scatter_PCs"].endswith(  # in case users are funny
+                PCA_CUSTOM_SCATTER_OUTER_SEPARATOR
+            ):
+                cfg["PCA_custom_scatter_PCs"] = cfg["PCA_custom_scatter_PCs"][:-1]
             start_string += "\n\nCustom Scatterplot Configuration:"
             for i, custom_scatter_PCs in enumerate(
                 cfg["PCA_custom_scatter_PCs"].split(PCA_CUSTOM_SCATTER_OUTER_SEPARATOR)
@@ -156,13 +161,17 @@ def ylabel_velocity_and_acceleration(feature, unit, sampling_rate):
 
 
 # %% ........................  misc. helper functions  .................................
-
-
-def write_issues_to_textfile(message, results_dir):
-    """Write issues to a textfile"""
-    issues_textfile = os.path.join(results_dir, ISSUES_TXT_FILENAME)
-    with open(issues_textfile, "a") as f:
-        f.write(message)
+def tukeys_only_info_message(folderinfo):
+    """Inform user about the fact that we are only doing Tukeys due to our ANOVA sanity check failing"""
+    tukeys_only_info_message = (
+        "\n***********\n! WARNING !\n***********\n\n"
+        + "Your ANOVA settings were wrong.This either happens because: \n 1) You ran "
+        + "a one-way ANOVA with wrong inputs (there should be another message about "
+        + "this) or \n 2) You attempted to run a two-way design which is not "
+        + "supported yet.\nWe will run Tukey's test for multiple comparisons anyways."
+    )
+    print(tukeys_only_info_message)
+    write_issues_to_textfile(tukeys_only_info_message, folderinfo)
 
 
 def check_mouse_conversion(feature, cfg, **kwargs):

autogaita-1.0.3/autogaita/gui/group_gui_config.json

@@ -0,0 +1,114 @@
+[
+    {
+        "group_names": [
+            "3m_5mm",
+            "3m_12mm",
+            "3m_25mm",
+            "",
+            "",
+            ""
+        ],
+        "group_dirs": [
+            "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/5mm/9w",
+            "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/12mm/9w",
+            "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/25mm/9w",
+            "",
+            "",
+            ""
+        ],
+        "results_dir": "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Full Dataset and Results Nov 2024/3m3BeamsForPaper"
+    },
+    {
+        "do_permtest": false,
+        "do_anova": true,
+        "anova_design": "RM ANOVA",
+        "permutation_number": "10000",
+        "stats_threshold": "0.05",
+        "which_leg": "right",
+        "PCA_n_components": "0.9",
+        "PCA_custom_scatter_PCs": "1,3;2,3;2,3,4;",
+        "PCA_save_3D_video": true,
+        "PCA_bins": "",
+        "plot_SE": true,
+        "color_palette": "inferno",
+        "dont_show_plots": false,
+        "legend_outside": true,
+        "stats_variables": [
+            "Hip x",
+            "Hip y",
+            "Knee x",
+            "Knee y",
+            "Ankle x",
+            "Ankle y",
+            "Hind paw tao x",
+            "Hind paw tao y",
+            "Hind paw tao Velocity",
+            "Ankle Velocity",
+            "Knee Velocity",
+            "Ankle Angle",
+            "Knee Angle",
+            "Hip Angle"
+        ],
+        "PCA_variables": [
+            "Nose x",
+            "Nose y",
+            "Ear base x",
+            "Ear base y",
+            "Front paw tao x",
+            "Front paw tao y",
+            "Wrist x",
+            "Wrist y",
+            "Elbow x",
+            "Elbow y",
+            "Lower Shoulder x",
+            "Lower Shoulder y",
+            "Upper Shoulder x",
+            "Upper Shoulder y",
+            "Iliac Crest x",
+            "Iliac Crest y",
+            "Hip x",
+            "Hip y",
+            "Knee x",
+            "Knee y",
+            "Ankle x",
+            "Ankle y",
+            "Hind paw tao x",
+            "Hind paw tao y",
+            "Tail base y",
+            "Tail center x",
+            "Tail center y",
+            "Tail tip x",
+            "Tail tip y",
+            "Hind paw tao Velocity",
+            "Hind paw tao Acceleration",
+            "Ankle Velocity",
+            "Ankle Acceleration",
+            "Knee Velocity",
+            "Knee Acceleration",
+            "Hip Velocity",
+            "Hip Acceleration",
+            "Iliac Crest Velocity",
+            "Iliac Crest Acceleration",
+            "Ankle Angle",
+            "Knee Angle",
+            "Hip Angle",
+            "Wrist Angle",
+            "Elbow Angle",
+            "Lower Shoulder Angle",
+            "Iliac Crest Angle",
+            "Ankle Angle Velocity",
+            "Ankle Angle Acceleration",
+            "Knee Angle Acceleration",
+            "Hip Angle Velocity",
+            "Hip Angle Acceleration",
+            "Wrist Angle Velocity",
+            "Wrist Angle Acceleration",
+            "Elbow Angle Velocity",
+            "Elbow Angle Acceleration",
+            "Lower Shoulder Angle Velocity",
+            "Lower Shoulder Angle Acceleration",
+            "Iliac Crest Angle Velocity",
+            "Iliac Crest Angle Acceleration"
+        ]
+    }
+]

{autogaita-1.0.2 → autogaita-1.0.3}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.2
+Version: 1.0.3
 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-1.0.2 → autogaita-1.0.3}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.0.2",  # rc == release candidate (before release is finished)
+    version="1.0.3",  # rc == release candidate (before release is finished)
     author="Mahan Hosseini",
     description="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.",
     packages=find_packages(),

autogaita-1.0.2/autogaita/batchrun_scripts/group_dlcrun.py

@@ -1,108 +0,0 @@
-import autogaita
-
-
-def group_dlcrun():
-    """
-    Batchrun script to run AutoGaitA Group for Results obtained with AutoGaitA DLC.
-    folderinfo & cfg dictionaries must be configured as explained in our documentation. See the "AutoGaitA without the GUI" section of our documentation for references to in-depth explanations to all dictionary keys (note that each key of dicts corresponds to some object in the AutoGaitA Group GUI)
-    """
-    # folderinfo
-    # => Note that length of folderinfo's group_names & group_dirs lists determines how #    many groups are compared.
-    # => Also note that indices must correspond (i.e., idx #    1's name will be used #    for dataset stored in group_dir's idx 1)
-    folderinfo = {}
-    folderinfo["group_names"] = [
-        # RM Dataset
-        "5mm",
-        "12mm",
-        "25mm",
-        # Interaction Issue Dataset
-        # "Control",
-        # "Silenced",
-        # Testing Dataset
-        # "one",
-        # "two",
-    ]
-    folderinfo["group_dirs"] = [
-        # --------------------------
-        # Full Dataset (39 subjects)
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control Full",
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced Full/",
-        # --------------------------
-        # Reduced Dataset (5 subjects)
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Control",
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Sanity Test Interaction Graziana/Result 10 joints/Silenced/",
-        # --------------------------
-        # Testing Dataset
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 1/",
-        # "/Users/mahan/sciebo/Research/AutoGaitA/Mouse/Testing/Group 2/",
-        # --------------------------
-        # RM Dataset (example data in repo)
-        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/5mm/Results/",
-        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/12mm/Results/",
-        "/Users/mahan/sciebo/PythonCode/gaita_repo/example data/25mm/Results/",
-    ]
-    folderinfo["results_dir"] = (
-        "/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/"
-    )
-    # cfg
-    cfg = {}
-    cfg["do_permtest"] = False  # True
-    cfg["do_anova"] = True
-    cfg["permutation_number"] = 100
-    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"] = ""
-    cfg["PCA_save_3D_video"] = False  # True
-    cfg["PCA_bins"] = ""  # "0-10,24,50-75"
-    cfg["stats_threshold"] = 0.05
-    cfg["plot_SE"] = False
-    cfg["color_palette"] = "viridis"
-    cfg["dont_show_plots"] = True
-    cfg["legend_outside"] = True
-    cfg["which_leg"] = "left"
-    cfg["anova_design"] = "RM ANOVA"
-    # 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",
-        # "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.group(folderinfo, cfg)
-
-
-# %% what happens if we just hit run
-if __name__ == "__main__":
-    group_dlcrun()

autogaita-1.0.2/autogaita/gui/group_gui_config.json

@@ -1,41 +0,0 @@
-[
-    {
-        "group_names": [
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
-        ],
-        "group_dirs": [
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
-        ],
-        "results_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": [
-        ]
-    }
-]