autogaita 1.0.0__tar.gz → 1.0.2__tar.gz

{autogaita-1.0.0 → autogaita-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.0
+Version: 1.0.2
 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-1.0.0 → autogaita-1.0.2}/README.md

@@ -11,7 +11,7 @@
 
 # Automated Gait Analysis in Python 🐸
 
-- AutoGaitA simplifies, accelerates, and standardises gait analyses after body posture tracking with [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) or 3D tracking methods such as [Simi Motion](http://www.simi.com/en/products/movement-analysis/simi-motion-2d3d.html?type=rss%2F). 
+- 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'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-1.0.0 → autogaita-1.0.2}/autogaita/batchrun_scripts/sleap_singlerun.py

@@ -15,7 +15,7 @@ def sleap_singlerun():
     )
     folderinfo["results_dir"] = ""
     folderinfo["sctable_filename"] = "Annotation Table"
-    folderinfo["data_string"] = ""
+    folderinfo["data_string"] = "_data"
     folderinfo["beam_string"] = ""
 
     # cfg

{autogaita-1.0.0 → autogaita-1.0.2}/autogaita/group/group_4_stats.py

@@ -600,7 +600,7 @@ def run_ANOVA(stats_df, stats_var, cfg):
 
     # unpack
     anova_design = cfg["anova_design"]
-    if "2-way" in anova_design:
+    if "2-way" in anova_design:  # not really 2-way, see below
         if "RM" in anova_design:
             factor_1_col = cfg["factor_1_col"]
             factor_2_col = cfg["factor_2_col"]
@@ -609,21 +609,24 @@ def run_ANOVA(stats_df, stats_var, cfg):
             between_factor_col = cfg["between_factor_col"]
 
     # ..............  NOTE FOR MYSELF @ 13.12.2024 before releasing v1  ................
-    # => 2-way ANOVAs are not yet supported since I wanted to take more time to test
-    #    it and confirm that it gives expected results.
-    # => There is a branch with it being almost developed - I stopped there with
+    # => 2-way ANOVAs are 3-way ANOVAs with 2 within and 1 between subjects factor
+    #    really
+    # => Not supported by Pinguin, likely need to switch to statsmodel's linear mixed
+    #    effects models if I want to support it
+    # => There is a branch with the it being almost developed - I stopped there with
     #    tests of valid user input (@ line 677 of definefeatures_window) which did not
     #    behave as expected
     # => Still decided to leave these lines here as they are because they do not
     #    affect anything really
-    # => Also don't forget that 2-way fully between ANOVAs are not supported by Pingouin
     if anova_design == "RM ANOVA":
-        result = stats_df.rm_anova(dv=stats_var, within=GROUP_COL, subject=ID_COL)
+        result = stats_df.rm_anova(
+            dv=stats_var, within=[SC_PERCENTAGE_COL, GROUP_COL], subject=ID_COL
+        )
     elif anova_design == "Mixed ANOVA":
         result = stats_df.mixed_anova(
             dv=stats_var,
-            between=GROUP_COL,
             within=SC_PERCENTAGE_COL,
+            between=GROUP_COL,
             subject=ID_COL,
         )
     elif anova_design == "2-way RM ANOVA":

{autogaita-1.0.0 → autogaita-1.0.2}/autogaita/group/group_main.py

@@ -13,8 +13,8 @@ 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, print_finish
-from autogaita.resources.utils import PlotPanel
+from autogaita.group.group_utils import print_start
+from autogaita.resources.utils import print_finish, PlotPanel
 import matplotlib
 import matplotlib.pyplot as plt
 

{autogaita-1.0.0 → autogaita-1.0.2}/autogaita/group/group_utils.py

@@ -118,14 +118,6 @@ def print_start(folderinfo, cfg):
         f.write(start_string)
 
 
-def print_finish(folderinfo):
-    """Inform the user about being done."""
-    print("\n***************************************************************")
-    print("*      GAITA FINISHED - YOUR RESULTS WERE STORED HERE:        *")
-    print(folderinfo["results_dir"])
-    print("***************************************************************")
-
-
 # %% ......................  plotting helper functions  ...........................
 def save_figures(figure, results_dir, figure_file_string):
     """Save figures as pngs to results_dir and as svgs to separate subfolders"""

{autogaita-1.0.0 → autogaita-1.0.2}/autogaita/resources/utils.py

@@ -27,7 +27,14 @@ def try_to_run_gaita(tracking_software, info, folderinfo, cfg, multirun_flag):
     # first print some info
     line_row = "-" * INFO_TEXT_WIDTH
     empty_row = " " * INFO_TEXT_WIDTH
-    message_1 = "G A I T A | S T A R T"
+    software_string = ""
+    if tracking_software == "DLC":
+        software_string = "D E E P L A B C U T"
+    elif tracking_software == "SLEAP":
+        software_string = "S L E A P"
+    elif tracking_software == "Universal 3D":
+        software_string = "U N I V E R S A L  3 D"
+    message_1 = f"A U T O G A I T A | {software_string}"
     message_2 = "Analysing"
     message_3 = info["name"]
     side_space_1 = " " * ((INFO_TEXT_WIDTH - len(message_1)) // 2)
@@ -111,12 +118,13 @@ def print_finish(info):
     """Print that we finished this program"""
     line_row = "-" * INFO_TEXT_WIDTH
     empty_row = " " * INFO_TEXT_WIDTH
-    finished_message_1 = "G A I T A | D O N E"
+    finished_message_1 = "A U T O G A I T A | D O N E"
     finished_message_2 = "Results are here"
     side_space_1 = " " * ((INFO_TEXT_WIDTH - len(finished_message_1)) // 2)
     side_space_2 = " " * ((INFO_TEXT_WIDTH - len(finished_message_2)) // 2)
     message = (
-        line_row
+        "\n\n\n"
+        + line_row
         + "\n"
         + side_space_1
         + finished_message_1
@@ -128,7 +136,7 @@ def print_finish(info):
         + finished_message_2
         + side_space_2
         + "\n"
-        + info["results_dir"]
+        + str(info["results_dir"])
         + "\n"
         + line_row
     )

{autogaita-1.0.0 → autogaita-1.0.2}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.0.0
+Version: 1.0.2
 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-1.0.0 → autogaita-1.0.2}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.0.0",  # rc == release candidate (before release is finished)
+    version="1.0.2",  # 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(),