autogaita 1.3.0__tar.gz → 1.3.1__tar.gz

{autogaita-1.3.0 → autogaita-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.3.0
+Version: 1.3.1
 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-1.3.0 → autogaita-1.3.1}/autogaita/common2D/common2D_1_preparation.py

@@ -45,6 +45,8 @@ def some_prep(tracking_software, info, folderinfo, cfg):
     subtract_beam = cfg["subtract_beam"]
     convert_to_mm = cfg["convert_to_mm"]
     pixel_to_mm_ratio = cfg["pixel_to_mm_ratio"]
+    x_sc_broken_threshold = cfg["x_sc_broken_threshold"]
+    y_sc_broken_threshold = cfg["y_sc_broken_threshold"]
     standardise_y_at_SC_level = cfg["standardise_y_at_SC_level"]
     invert_y_axis = cfg["invert_y_axis"]
     flip_gait_direction = cfg["flip_gait_direction"]
@@ -196,7 +198,11 @@ def some_prep(tracking_software, info, folderinfo, cfg):
     config_vars_to_json = {
         "sampling_rate": sampling_rate,
         "convert_to_mm": convert_to_mm,
+        "pixel_to_mm_ratio": pixel_to_mm_ratio,
+        "x_sc_broken_threshold": x_sc_broken_threshold,
+        "y_sc_broken_threshold": y_sc_broken_threshold,
         "standardise_y_at_SC_level": standardise_y_at_SC_level,
+        "flip_gait_direction": flip_gait_direction,
         "analyse_average_x": analyse_average_x,
         "standardise_x_coordinates": standardise_x_coordinates,
         "x_standardisation_joint": x_standardisation_joint,
@@ -402,11 +408,20 @@ def check_this_filename_configuration(
     prerun_string = folderinfo["prerun_string"]
     whichvideo = ""  # initialise
     found_it = False
+    # handle leading zeros that we identified previously - if none convert nums to str
+    if "leading_mouse_num_zeros" in info.keys():
+        mouse_num = info["leading_mouse_num_zeros"] + str(mouse_num)
+    else:
+        mouse_num = str(mouse_num)
+    if "leading_run_num_zeros" in info.keys():
+        run_num = info["leading_run_num_zeros"] + str(run_num)
+    else:
+        run_num = str(run_num)
     for filename in os.listdir(root_dir):
         # the following condition is True for data & beam csv
         if (
-            (premouse_string + str(mouse_num) + postmouse_string in filename)
-            and (prerun_string + str(run_num) + postrun_string in filename)
+            (premouse_string + mouse_num + postmouse_string in filename)
+            and (prerun_string + run_num + postrun_string in filename)
             and (filename.endswith(file_type_string))
         ):
             found_it = True

{autogaita-1.3.0 → autogaita-1.3.1}/autogaita/common2D/common2D_utils.py

@@ -64,7 +64,7 @@ def extract_info(tracking_software, folderinfo, in_GUI=False):
             for string_addition in FILE_ID_STRING_ADDITIONS:
                 try:
                     candidate_postmouse_string = string_addition + postmouse_string
-                    this_mouse_num = find_number(
+                    this_mouse_num, leading_mouse_num_zeros = find_number(
                         filename,
                         premouse_string,
                         candidate_postmouse_string,
@@ -87,7 +87,7 @@ def extract_info(tracking_software, folderinfo, in_GUI=False):
             for string_addition in FILE_ID_STRING_ADDITIONS:
                 try:
                     candidate_postrun_string = string_addition + postrun_string
-                    this_run_num = find_number(
+                    this_run_num, leading_run_num_zeros = find_number(
                         filename, prerun_string, candidate_postrun_string
                     )
                 except:
@@ -109,6 +109,14 @@ def extract_info(tracking_software, folderinfo, in_GUI=False):
                     info["name"].append(this_name)
                     info["mouse_num"].append(this_mouse_num)
                     info["run_num"].append(this_run_num)
+    # if we had to fix leading zeros, make sure to save them so we can use them in
+    # move_data_to_folders function later
+    # => make sure it's lists of strings because this is needed by the
+    #    run_singlerun_in_multiruns function later
+    if leading_mouse_num_zeros:
+        info["leading_mouse_num_zeros"] = [leading_mouse_num_zeros]
+    if leading_run_num_zeros:
+        info["leading_run_num_zeros"] = [leading_run_num_zeros]
     # this might happen if user entered wrong identifiers or folder
     if len(info["name"]) < 1:
         no_files_message = (
@@ -146,7 +154,12 @@ def find_number(fullstring, prestring, poststring):
     """Find (mouse/run) number based on user-defined strings in filenames"""
     start_idx = fullstring.find(prestring) + len(prestring)
     end_idx = fullstring.find(poststring)
-    return int(fullstring[start_idx:end_idx])
+    # handle leading zeros
+    leading_zeros = ""
+    while fullstring[start_idx] == "0" and start_idx < end_idx - 1:
+        start_idx += 1
+        leading_zeros += "0"
+    return int(fullstring[start_idx:end_idx]), leading_zeros
 
 
 # ...........................  SC extraction helpers  ..................................

{autogaita-1.3.0 → autogaita-1.3.1}/autogaita/group/group_1_preparation.py

@@ -28,10 +28,11 @@ def some_prep(folderinfo, cfg):
     # Alright so the group pipeline's cfg (and thus, of course, config.json) is a bit
     # special because it includes:
     # 1) first-level config-keys, such as "joints" or "angles", that reflect what has
-    #    been analysed at the first level. These are also checked for equivalence
-    #    across groups when running this without load_dir (see the for g_idx loop
-    #    below) to ensure we are not comparing different sampling rates or so with a
-    #    group analysis
+    #    been analysed at the first level. Some of these are used in group workflow
+    #    (e.g. tracking_software when plotting or sampling_rate for PCA) and all of
+    #    these are  checked for equivalence across groups when running this without
+    #    load_dir (see the for g_idx loop below) to ensure we are not comparing
+    #    different sampling rates or so with a group analysis
     # 2) group-level config-keys, such as "do_permtest" or "PCA_variables" that define
     #    how group analysis should be done
     # Now:
@@ -145,14 +146,20 @@ def some_prep(folderinfo, cfg):
 
 
 def load_previous_runs_first_level_cfg_vars(folderinfo, cfg):
-    """There are only a few "first-level" cfg vars (like "joints") we require for group gaita's workflow - load them here"""
+    """There are a couple "first-level" cfg vars (like "joints") we require for group gaita's workflow - load them here"""
     with open(
         os.path.join(folderinfo["load_dir"], CONFIG_JSON_FILENAME), "r"
     ) as config_json_file:
         old_cfg = json.load(config_json_file)
+        cfg["sampling_rate"] = old_cfg["sampling_rate"]
         cfg["save_to_xls"] = old_cfg["save_to_xls"]
         cfg["joints"] = old_cfg["joints"]
         cfg["angles"] = old_cfg["angles"]
+        cfg["tracking_software"] = old_cfg["tracking_software"]
+        if "analyse_average_x" in old_cfg.keys():
+            cfg["analyse_average_x"] = old_cfg["analyse_average_x"]
+        if "analyse_average_y" in old_cfg.keys():
+            cfg["analyse_average_y"] = old_cfg["analyse_average_y"]
     return cfg
 
 

{autogaita-1.3.0 → autogaita-1.3.1}/autogaita/gui/group_gui.py

@@ -12,7 +12,6 @@ import platform
 import json
 import copy
 
-
 # %% global constants
 from autogaita.gui.gui_constants import (
     GROUP_FG_COLOR,
@@ -917,7 +916,7 @@ def check_folderinfo_and_cfg(folderinfo, cfg):
         for key in inner_dict.keys():
             # check string vars: group dirs & names and results dir
             if key in STRING_VARS:
-                if key == "group_dirs" and len(folderinfo["load_dir"]) > 0:
+                if key == "group_dirs" and len(folderinfo["load_dir"]) == 0:
                     for g_idx, group_dir in enumerate(inner_dict[key]):
                         if not os.path.exists(group_dir):
                             this_msg = (

{autogaita-1.3.0 → autogaita-1.3.1}/autogaita/universal3D/universal3D_1_preparation.py

@@ -30,6 +30,7 @@ def some_prep(info, folderinfo, cfg):
     results_dir = info["results_dir"]
     postname_string = folderinfo["postname_string"]
     sampling_rate = cfg["sampling_rate"]
+    flip_gait_direction = cfg["flip_gait_direction"]
     standardise_z_at_SC_level = cfg["standardise_z_at_SC_level"]
     analyse_average_y = cfg["analyse_average_y"]
     standardise_y_coordinates = cfg["standardise_y_coordinates"]
@@ -122,6 +123,7 @@ def some_prep(info, folderinfo, cfg):
     config_json_path = os.path.join(group_path, CONFIG_JSON_FILENAME)
     config_vars_to_json = {
         "sampling_rate": sampling_rate,
+        "flip_gait_direction": flip_gait_direction,
         "standardise_z_at_SC_level": standardise_z_at_SC_level,
         "analyse_average_y": analyse_average_y,
         "standardise_y_coordinates": standardise_y_coordinates,

{autogaita-1.3.0 → autogaita-1.3.1}/autogaita.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 1.3.0
+Version: 1.3.1
 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-1.3.0 → autogaita-1.3.1}/autogaita.egg-info/SOURCES.txt

@@ -77,6 +77,7 @@ tests/__init__.py
 tests/test_common2D_unit_1_preparation.py
 tests/test_common2D_unit_2_sc_extraction.py
 tests/test_common2D_unit_3_analysis.py
+tests/test_common2D_unit_utils.py
 tests/test_dlc_approval.py
 tests/test_dlc_unit_1_preparation.py
 tests/test_group_approval.py

{autogaita-1.3.0 → autogaita-1.3.1}/setup.py

@@ -26,7 +26,7 @@ if platform.system() == "Darwin":
 setup(
     name="autogaita",
     python_requires=">=3.10",
-    version="1.3.0",  # rc == release candidate (before release is finished)
+    version="1.3.1",  # 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-1.3.1/tests/test_common2D_unit_1_preparation.py

@@ -0,0 +1,334 @@
+from autogaita.common2D.common2D_1_preparation import (
+    move_data_to_folders,
+    check_and_expand_cfg,
+    check_and_fix_cfg_strings,
+    flip_mouse_body,
+    some_prep,  # note that first input of some_prep is set to "DLC" when not mattering!
+)
+from autogaita.common2D.common2D_utils import extract_info
+import os
+import copy
+import math
+import numpy as np
+import pandas.testing as pdt
+from hypothesis import given, strategies as st, settings, HealthCheck
+import pytest
+
+
+# %%..............................  fixtures  ..........................................
+# NOTE
+# ----
+# Calling them FIXTURE_extract_... since we have a function called extract_info!
+
+
+@pytest.fixture
+def extract_data_using_some_prep(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    return data
+
+
+@pytest.fixture
+def fixture_extract_info(tmp_path):
+    info = {}
+    info["mouse_num"] = 15
+    info["run_num"] = 3
+    info["name"] = "ID " + str(info["mouse_num"]) + " - Run " + str(info["run_num"])
+    info["results_dir"] = os.path.join(tmp_path, info["name"])
+    return info
+
+
+@pytest.fixture
+def fixture_extract_folderinfo():
+    folderinfo = {}
+    folderinfo["root_dir"] = "tests/test_data/dlc_data"
+    folderinfo["sctable_filename"] = (
+        "correct_annotation_table.xlsx"  # has to be an excel file
+    )
+    folderinfo["data_string"] = "SIMINewOct"
+    folderinfo["beam_string"] = "BeamTraining"
+    folderinfo["premouse_string"] = "Mouse"
+    folderinfo["postmouse_string"] = "25mm"
+    folderinfo["prerun_string"] = "run"
+    folderinfo["postrun_string"] = "6DLC"
+    return folderinfo
+
+
+@pytest.fixture
+def fixture_extract_cfg():
+    cfg = {}
+    cfg["sampling_rate"] = 100
+    cfg["subtract_beam"] = True
+    cfg["dont_show_plots"] = True
+    cfg["convert_to_mm"] = True
+    cfg["pixel_to_mm_ratio"] = 3.76
+    cfg["x_sc_broken_threshold"] = 200
+    cfg["y_sc_broken_threshold"] = 50
+    cfg["x_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["save_to_xls"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_y_at_SC_level"] = False
+    cfg["standardise_y_to_a_joint"] = True
+    cfg["y_standardisation_joint"] = ["Knee"]
+    cfg["plot_joint_number"] = 3
+    cfg["color_palette"] = "viridis"
+    cfg["legend_outside"] = True
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_x"] = True
+    cfg["standardise_x_coordinates"] = True
+    cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = ""
+    cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
+    cfg["fore_joints"] = [
+        "Front paw tao ",
+        "Wrist ",
+        "Elbow ",
+        "Lower Shoulder ",
+        "Upper Shoulder ",
+    ]
+    cfg["beam_col_left"] = ["BeamLeft"]  # BEAM_COL_LEFT & _RIGHT must be lists of len=1
+    cfg["beam_col_right"] = ["BeamRight"]
+    cfg["beam_hind_jointadd"] = ["Tail base ", "Tail center ", "Tail tip "]
+    cfg["beam_fore_jointadd"] = ["Nose ", "Ear base "]
+    cfg["angles"] = {
+        "name": ["Ankle ", "Knee ", "Hip "],
+        "lower_joint": ["Hind paw tao ", "Ankle ", "Knee "],
+        "upper_joint": ["Knee ", "Hip ", "Iliac Crest "],
+    }
+    return cfg
+
+
+# %%..............................  preparation  .......................................
+#                       AN IMPORTANT NOTE ON THESE UNIT TESTS!
+# Calling check_and_expand cfg outside of some_prep with the
+# export_data_using_some_prep fixture leads to the cfg that is returned by
+# check_and_expand to be None since the data var DOES NOT INCLUDE the beam!
+# => We thus set cfg["subtract_beam"] to False prior to calling it (see e.g.the
+#    plot_joint test)
+
+
+def test_move_data_to_folders_smoke_normal(
+    fixture_extract_info, fixture_extract_folderinfo
+):
+    move_data_to_folders(
+        "DLC", ".csv", fixture_extract_info, fixture_extract_folderinfo
+    )
+    assert len(os.listdir(fixture_extract_info["results_dir"])) == 3
+    for file in os.listdir(fixture_extract_info["results_dir"]):
+        if file.endswith(".csv"):
+            assert (
+                (fixture_extract_folderinfo["premouse_string"] in file)
+                & (fixture_extract_folderinfo["postmouse_string"] in file)
+                & (fixture_extract_folderinfo["prerun_string"] in file)
+                & (fixture_extract_folderinfo["postrun_string"] in file)
+            )
+
+
+def test_move_data_to_folders_leading_zeros_handled(
+    tmp_path, fixture_extract_folderinfo
+):
+    # ensure files with leading zeros are moved too
+    # => this needs some preparation because I want to test extract_info, too, which is
+    #    required to output lists in each of its keys because I use it in multiruns to
+    #    iterate over each idxs which consistute separate runs
+    fixture_extract_folderinfo["root_dir"] = (
+        "tests/test_data/dlc_data/test_data/leading_zeros/"
+    )
+    # CARE! function: extract_info for info where we handle leading zeros
+    info = extract_info("DLC", fixture_extract_folderinfo)
+    info["results_dir"] = tmp_path
+    # move_data... creates it, make sure it's not there
+    if os.path.exists(info["results_dir"]):
+        for file in os.listdir(info["results_dir"]):
+            os.remove(os.path.join(info["results_dir"], file))
+        os.rmdir(info["results_dir"])
+    # now make sure info is not a list
+    for key in info:
+        if isinstance(info[key], list):
+            info[key] = info[key][0]
+    move_data_to_folders("DLC", ".csv", info, fixture_extract_folderinfo)
+    assert len(os.listdir(info["results_dir"])) == 2
+
+
+# %%..........................  cfg & string stuff  ....................................
+def test_plot_joint_error(
+    extract_data_using_some_prep, fixture_extract_cfg, fixture_extract_info
+):
+    fixture_extract_cfg["plot_joint_number"] = 2000
+    fixture_extract_cfg["subtract_beam"] = False
+    check_and_expand_cfg(
+        extract_data_using_some_prep, fixture_extract_cfg, fixture_extract_info
+    )
+    with open(os.path.join(fixture_extract_info["results_dir"], "Issues.txt")) as f:
+        content = f.read()
+    assert "we can :)" in content
+    fixture_extract_cfg = check_and_expand_cfg(
+        extract_data_using_some_prep, fixture_extract_cfg, fixture_extract_info
+    )
+    assert fixture_extract_cfg["plot_joints"] == fixture_extract_cfg["hind_joints"]
+    fixture_extract_cfg["plot_joint_number"] = 2
+    fixture_extract_cfg = check_and_expand_cfg(
+        extract_data_using_some_prep, fixture_extract_cfg, fixture_extract_info
+    )
+    assert fixture_extract_cfg["plot_joints"] == fixture_extract_cfg["hind_joints"][:2]
+
+
+def test_error_if_no_cfgkey_joints(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    full_cfg = copy.deepcopy(
+        fixture_extract_cfg
+    )  # no referencing here - we need copies!
+    for cfg_key in [
+        "hind_joints",
+        "x_standardisation_joint",
+        "y_standardisation_joint",
+    ]:
+        fixture_extract_cfg = copy.deepcopy(full_cfg)  # here too!
+        fixture_extract_cfg[cfg_key] = ["not_in_data"]
+        data = some_prep(
+            "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+        )
+        with open(os.path.join(fixture_extract_info["results_dir"], "Issues.txt")) as f:
+            content = f.read()
+        if cfg_key == "hind_joints":
+            assert "hind limb joint names" in content
+        elif cfg_key == "x_standardisation_joint":
+            assert "x-coordinate standardisation joint" in content
+        elif cfg_key == "y_standardisation_joint":
+            assert "y-coordinate standardisation joint" in content
+        assert data is None
+    # cannot loop case of x & y joints being broken
+    fixture_extract_cfg = copy.deepcopy(full_cfg)
+    fixture_extract_cfg["x_standardisation_joint"] = ["not_in_data"]
+    fixture_extract_cfg["y_standardisation_joint"] = ["not_in_data"]
+    data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    with open(os.path.join(fixture_extract_info["results_dir"], "Issues.txt")) as f:
+        content = f.read()
+        assert "x & y-coordinate standardisation joint" in content
+        assert data is None
+
+
+@given(test_list=st.lists(st.text(), min_size=1))
+@settings(suppress_health_check=[HealthCheck.function_scoped_fixture])
+def test_removal_of_wrong_strings_from_cfg_key(
+    test_list, extract_data_using_some_prep, fixture_extract_cfg, fixture_extract_info
+):
+    # the following loop is to account for hypothesis randomly generating strings that
+    # actually are data columns (happend for "Knee ")
+    for i in range(len(test_list)):
+        if test_list[i] + "x" in extract_data_using_some_prep.columns:
+            test_list.pop(i)
+    cfg_key = "hind_joints"  # irrelevant since property testing
+    fixture_extract_cfg[cfg_key] = test_list
+    test_result = check_and_fix_cfg_strings(
+        extract_data_using_some_prep, fixture_extract_cfg, cfg_key, fixture_extract_info
+    )
+    assert not test_result  # empty list is falsey
+
+
+def test_wrong_data_and_beam_strings(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    fixture_extract_folderinfo["beam_string"] = fixture_extract_folderinfo[
+        "data_string"
+    ]
+    some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    with open(os.path.join(fixture_extract_info["results_dir"], "Issues.txt")) as f:
+        content = f.read()
+    assert "Your data & baseline (beam) identifiers ([G] in our" in content
+
+
+def test_wrong_postmouse_string(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    fixture_extract_folderinfo["postmouse_string"] = "this_is_a_test"
+    some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    with open(os.path.join(fixture_extract_info["results_dir"], "Issues.txt")) as f:
+        content = f.read()
+    assert "Unable to identify ANY RELEVANT FILES for" in content
+
+
+# %%...........................  dataframe stuff  ......................................
+def test_cols_we_added_to_data(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    assert (data.columns[0] == "Time") & (data.columns[1] == "Flipped")
+
+
+def test_datas_indexing_and_time_column(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    for fixture_extract_cfg["sampling_rate"] in [50, 500, 5000]:
+        data = some_prep(
+            "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+        )
+        # use isclose here because there are some floating point things going on (eg. 1.
+        # 66 and 1.660 for sampling rate of 500)
+        assert math.isclose(
+            data["Time"].max(),
+            (len(data) - 1) / (1 * fixture_extract_cfg["sampling_rate"]),
+            rel_tol=1e-9,
+        )
+
+
+# %%...........................  data manipulation  ....................................
+def test_global_min_standardisation(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    fixture_extract_cfg["subtract_beam"] = False
+    fixture_extract_cfg["standardise_y_to_a_joint"] = False
+    data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    y_cols = [c for c in data.columns if c.endswith(" y")]
+    assert data[y_cols].min().min() == 0
+    # approach here is find difference between global & standardisation joint minma and
+    # see if all y cols' difference is equal to that
+    # => this implies that joint-based y-standardisation worked
+    global_and_standardisation_joints_y_min_diff = data[
+        fixture_extract_cfg["y_standardisation_joint"][0] + " y"
+    ].min()
+    global_min_data = data.copy()
+    fixture_extract_cfg["standardise_y_to_a_joint"] = True
+    data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    assert np.allclose(  # use np.allclose here because we are comparing arrays
+        global_min_data[y_cols],
+        data[y_cols] + global_and_standardisation_joints_y_min_diff,
+        atol=1e-9,
+    )
+
+
+def test_flip_mouse_body(
+    fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+):
+    fixture_extract_cfg["flip_gait_direction"] = False
+    test_data = some_prep(
+        "DLC", fixture_extract_info, fixture_extract_folderinfo, fixture_extract_cfg
+    )
+    function_flipped_data = test_data.copy()
+    function_flipped_data = flip_mouse_body(test_data, fixture_extract_info)
+    x_cols = [col for col in function_flipped_data.columns if col.endswith(" x")]
+    global_x_max = max(test_data[x_cols].max())
+    for col in x_cols:
+        function_flipped_series = function_flipped_data[col]
+        function_flipped_series = function_flipped_series.astype(float)
+        manually_flipped_series = global_x_max - test_data[col]
+        pdt.assert_series_equal(function_flipped_series, manually_flipped_series)

autogaita-1.3.1/tests/test_common2D_unit_utils.py

@@ -0,0 +1,134 @@
+import pytest
+from autogaita.common2D.common2D_utils import extract_info, find_number
+import os
+import pytest
+
+
+# %%..............................  fixtures  ..........................................
+# => CALL FIXTURES _fixture SINCE WE HAVE A FUNCTION CALLED extract_info!
+@pytest.fixture
+def fixture_extract_info(tmp_path):
+    info = {}
+    info["mouse_num"] = 15
+    info["run_num"] = 3
+    info["name"] = "ID " + str(info["mouse_num"]) + " - Run " + str(info["run_num"])
+    info["results_dir"] = os.path.join(tmp_path, info["name"])
+    return info
+
+
+@pytest.fixture
+def fixture_extract_folderinfo():
+    folderinfo = {}
+    folderinfo["root_dir"] = "tests/test_data/dlc_data"
+    folderinfo["sctable_filename"] = (
+        "correct_annotation_table.xlsx"  # has to be an excel file
+    )
+    folderinfo["data_string"] = "SIMINewOct"
+    folderinfo["beam_string"] = "BeamTraining"
+    folderinfo["premouse_string"] = "Mouse"
+    folderinfo["postmouse_string"] = "_25mm"
+    folderinfo["prerun_string"] = "run"
+    folderinfo["postrun_string"] = "-6DLC"
+    return folderinfo
+
+
+@pytest.fixture
+def fixture_extract_cfg():
+    cfg = {}
+    cfg["sampling_rate"] = 100
+    cfg["subtract_beam"] = True
+    cfg["dont_show_plots"] = True
+    cfg["convert_to_mm"] = True
+    cfg["pixel_to_mm_ratio"] = 3.76
+    cfg["x_sc_broken_threshold"] = 200
+    cfg["y_sc_broken_threshold"] = 50
+    cfg["x_acceleration"] = True
+    cfg["angular_acceleration"] = True
+    cfg["save_to_xls"] = True
+    cfg["bin_num"] = 25
+    cfg["plot_SE"] = True
+    cfg["standardise_y_at_SC_level"] = False
+    cfg["standardise_y_to_a_joint"] = True
+    cfg["y_standardisation_joint"] = ["Knee"]
+    cfg["plot_joint_number"] = 3
+    cfg["color_palette"] = "viridis"
+    cfg["legend_outside"] = True
+    cfg["invert_y_axis"] = True
+    cfg["flip_gait_direction"] = True
+    cfg["analyse_average_x"] = True
+    cfg["standardise_x_coordinates"] = True
+    cfg["x_standardisation_joint"] = ["Hind paw tao"]
+    cfg["coordinate_standardisation_xls"] = ""
+    cfg["hind_joints"] = ["Hind paw tao", "Ankle", "Knee", "Hip", "Iliac Crest"]
+    cfg["fore_joints"] = [
+        "Front paw tao ",
+        "Wrist ",
+        "Elbow ",
+        "Lower Shoulder ",
+        "Upper Shoulder ",
+    ]
+    cfg["beam_col_left"] = ["BeamLeft"]  # BEAM_COL_LEFT & _RIGHT must be lists of len=1
+    cfg["beam_col_right"] = ["BeamRight"]
+    cfg["beam_hind_jointadd"] = ["Tail base ", "Tail center ", "Tail tip "]
+    cfg["beam_fore_jointadd"] = ["Nose ", "Ear base "]
+    cfg["angles"] = {
+        "name": ["Ankle ", "Knee ", "Hip "],
+        "lower_joint": ["Hind paw tao ", "Ankle ", "Knee "],
+        "upper_joint": ["Knee ", "Hip ", "Iliac Crest "],
+    }
+    return cfg
+
+
+# %%..............................  tests  ..........................................
+# 1) Test extract_info function
+def test_extract_info_function(fixture_extract_folderinfo):
+    # => IT IS CORRECT THAT EXTRACT_INFO RETURNS lists of integers!
+    # a. smoke test standard case
+    info = extract_info("DLC", fixture_extract_folderinfo)
+    assert info["mouse_num"] == [15]
+    assert info["run_num"] == [3]
+    # b. test that underscores/hyphens are added
+    folderinfo = fixture_extract_folderinfo
+    folderinfo["postmouse_string"] = "25mm"
+    folderinfo["postrun_string"] = "6DLC"
+    info = extract_info("DLC", folderinfo)
+    assert info["mouse_num"] == [15]
+    assert info["run_num"] == [3]
+    # c. test that leading zeros are removed
+    folderinfo["root_dir"] = "tests/test_data/dlc_data/test_data/leading_zeros/"
+    info = extract_info("DLC", folderinfo)
+    assert info["mouse_num"] == [12]
+    assert info["run_num"] == [3]
+
+
+# 2) Test find number function - also for leading zeros
+def test_find_number_valid_case():
+    fullstring = "Mouse1_Run002"
+    prestring = "Mouse"
+    poststring = "_Run"
+    result = find_number(fullstring, prestring, poststring)
+    assert result == (1, "")
+
+
+def test_find_number_prestring_not_found():
+    fullstring = "Mouse001_Run002"
+    prestring = "Cat"
+    poststring = "_Run"
+    with pytest.raises(ValueError):
+        find_number(fullstring, prestring, poststring)
+
+
+def test_find_number_poststring_not_found():
+    fullstring = "Mouse001_Run002"
+    prestring = "Mouse"
+    poststring = "_Walk"
+    with pytest.raises(ValueError):
+        find_number(fullstring, prestring, poststring)
+
+
+def test_find_number_leading_zeros():
+    fullstring = "Mouse001Run002"
+    prestring = "Mouse"
+    poststring = "Run"
+    result = find_number(fullstring, prestring, poststring)
+    assert result == (1, "00")