autogaita 1.5.2__py3-none-any.whl → 1.5.4__py3-none-any.whl

tests/test_common2D_unit_utils.py

@@ -1,137 +0,0 @@
-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, 12]
-    # order of this might break in some test env
-    assert info["run_num"] == [4, 3]
-    assert info["leading_mouse_num_zeros"] == [False, False]
-    assert info["leading_run_num_zeros"] == ["00", False]
-
-
-# 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, False)
-
-
-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")

tests/test_dlc_approval.py

@@ -1,110 +0,0 @@
-from autogaita.resources.utils import try_to_run_gaita
-import pandas as pd
-import pandas.testing as pdt
-import os
-import pytest
-
-# ............................  DLC APPROVAL TESTS STRUCTURE  ..........................
-# 1. Run 4 pytest fixtures in preparation
-# 2. Run autogaita.dlc for ID 15 - Run 3 (with the cfg used there)
-# 3. Load the "Average Stepcycles".xlsx file from the repo and compare for
-#    equivalence to average_data
-# 4. Do the same for "Standard Devs. Stepcycle.xlsx" and std_data
-# 5. Pass the test if the two df-pairs are equal
-
-
-# ...............................  PREPARE - FOUR FIXTURES   ...........................
-
-
-@pytest.fixture
-def extract_true_dir():
-    return "tests/test_data/dlc_data/true_data/"
-
-
-@pytest.fixture
-def extract_info(tmp_path):
-    info = {}
-    info["mouse_num"] = 12
-    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 extract_folderinfo():
-    folderinfo = {}
-    folderinfo["root_dir"] = "tests/test_data/dlc_data/test_data/"
-    folderinfo["sctable_filename"] = "correct_annotation_table.xlsx"
-    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 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
-
-
-# ..............................  RUN - ONE APPROVAL TESTS  ............................
-
-
-@pytest.mark.slow
-def test_dlc_approval_average_df(
-    extract_true_dir, extract_info, extract_folderinfo, extract_cfg
-):
-    # run
-    try_to_run_gaita("DLC", extract_info, extract_folderinfo, extract_cfg, False)
-    for true_df_file in os.listdir(extract_true_dir):
-        if true_df_file.endswith(".xlsx"):
-            true_df = pd.read_excel(os.path.join(extract_true_dir, true_df_file))
-            test_df = pd.read_excel(
-                os.path.join(extract_info["results_dir"], true_df_file)
-            )
-            pdt.assert_frame_equal(test_df, true_df)

tests/test_dlc_unit_1_preparation.py

@@ -1,114 +0,0 @@
-from autogaita.common2D.common2D_1_preparation import (
-    some_prep,
-    move_data_to_folders,
-    check_gait_direction,
-)
-import os
-import pandas as pd
-import pytest
-
-
-# %%................................  fixtures  ........................................
-@pytest.fixture
-def extract_data_using_some_prep(extract_info, extract_folderinfo, extract_cfg):
-    data = some_prep("DLC", extract_info, extract_folderinfo, extract_cfg)
-    return data
-
-
-@pytest.fixture
-def 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 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 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  .......................................
-def test_check_gait_direction(extract_data_using_some_prep, extract_cfg, extract_info):
-    direction_joint = extract_cfg["direction_joint"]
-    flip_gait_direction = True  # 1) test broken DLC data (empty)
-    broken_data = pd.DataFrame(data=None, columns=extract_data_using_some_prep.columns)
-    check_gait_direction(
-        "DLC", broken_data, direction_joint, flip_gait_direction, extract_info
-    )
-    with open(os.path.join(extract_info["results_dir"], "Issues.txt")) as f:
-        content = f.read()
-    assert "Unable to determine gait direction!" in content
-    flip_this_data = pd.DataFrame(
-        data=None, columns=extract_data_using_some_prep.columns
-    )  # 2) test data that has to be flipped
-    data_len = 20
-    flip_this_data[direction_joint + "likelihood"] = [0.99] * data_len
-    first_half = [10] * int((data_len / 2))
-    second_half = [-10] * int((data_len / 2))
-    x_coords = first_half + second_half
-    flip_this_data[direction_joint + "x"] = x_coords
-    flip_this_data = check_gait_direction(
-        "DLC", flip_this_data, direction_joint, flip_gait_direction, extract_info
-    )
-    assert flip_this_data["Flipped"][0] == True

tests/test_group_approval.py

@@ -1,162 +0,0 @@
-from autogaita import group
-from autogaita.group.group_constants import STATS_TXT_FILENAME
-from autogaita.resources.constants import CONFIG_JSON_FILENAME
-import pandas as pd
-import pandas.testing as pdt
-import filecmp
-import os
-import shutil
-import pdb
-import pytest
-
-# ...........................  GROUP APPROVAL TESTS STRUCTURE  .........................
-# 1. Run autogaita.group for example group (3 beams) data (with the cfg used there)
-#    store results in a temporary path using tmp_path input.
-# 2. Load the "Grand Average Stepcycles".xlsx & "Grand Standard Devs. Stepcycle.xlsx"
-#    files from the repo (TRUE PATH) - test for equivalence with TEST PATH
-# 3. Then test if PCA XLS file is equal
-# 4. Finally test if Stats.txt files are equal
-
-# A Note
-# ------
-# We don't test the cluster extent test in an automated way.
-# We have results of simulations that ran for over a week in our preprint.
-# If the cluster extent test should change for some reason - re-run those simulations.
-
-
-# ...............................  PREPARE - THREE FIXTURES   ..........................
-
-
-@pytest.fixture
-def extract_true_dir():
-    return "example data/group/"
-
-
-@pytest.fixture
-def extract_folderinfo(tmp_path):
-    folderinfo = {}
-    folderinfo["group_names"] = ["5 mm", "12 mm", "25 mm"]
-    folderinfo["group_dirs"] = [
-        "example data/5mm/Results/",
-        "example data/12mm/Results/",
-        "example data/25mm/Results/",
-    ]
-    folderinfo["results_dir"] = tmp_path
-    folderinfo["load_dir"] = ""
-    return folderinfo
-
-
-@pytest.fixture
-def extract_cfg():
-    cfg = {}
-    cfg["do_permtest"] = False
-    cfg["do_anova"] = True
-    cfg["permutation_number"] = 100
-    cfg["PCA_n_components"] = 3
-    cfg["PCA_custom_scatter_PCs"] = ""
-    cfg["PCA_save_3D_video"] = False
-    cfg["PCA_bins"] = ""
-    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["permutation_number"] = 100
-    # NOTE - PCA & stats lists MUST be kept in this order
-    # (otherwise PCA.Info & Stats.txt wont be equivalent to TRUE_DATA's)
-    # => it's this order because it resulted from group_gui input (and thus corresponds to the checkbox-order of the features window)
-    cfg["PCA_variables"] = [
-        "Knee y",
-        "Ankle y",
-        "Hind paw tao y",
-        "Ankle Angle",
-        "Knee Angle",
-        "Hip Angle",
-    ]
-    cfg["stats_variables"] = cfg["PCA_variables"]
-    return cfg
-
-
-# ..............................  RUN - ONE APPROVAL TEST  .............................
-
-
-@pytest.mark.filterwarnings("ignore:Epsilon values")
-@pytest.mark.slow
-def test_group_approval(extract_true_dir, extract_folderinfo, extract_cfg):
-
-    # ...........................  1) RUN GROUP GAITA  .................................
-    group(extract_folderinfo, extract_cfg)
-
-    # ......................  2) TEST EQUIVALENCE OF GROUP DFs  ........................
-    # load true dfs from xlsx files
-    true_av_df = pd.read_excel(
-        os.path.join(extract_true_dir, "25 mm - Grand Average Group Stepcycles.xlsx")
-    )
-    true_std_df = pd.read_excel(
-        os.path.join(
-            extract_true_dir, "25 mm - Grand Standard Deviation Group Stepcycles.xlsx"
-        )
-    )
-    test_av_df = pd.read_excel(
-        os.path.join(
-            extract_folderinfo["results_dir"],
-            "25 mm - Grand Average Group Stepcycles.xlsx",
-        )
-    )
-    test_std_df = pd.read_excel(
-        os.path.join(
-            extract_folderinfo["results_dir"],
-            "25 mm - Grand Standard Deviation Group Stepcycles.xlsx",
-        )
-    )
-    # finally assert equivalence of df-pairs
-    pdt.assert_frame_equal(test_av_df, true_av_df)
-    pdt.assert_frame_equal(test_std_df, true_std_df)
-
-    # .......................  3) TEST EQUIVALENCE OF PCA DFs  .........................
-    # => okay so the equivalence test fails for ID INFO.xlsx on CI but passes locally.
-    # => it is due to the rows of the ID INFO.xlsx being in a different order
-    # => I guess due to how git-actions' os lists the files in the folder or something
-    # => the workaround here uses a env-variable that is set in the CI workflow file
-    if os.getenv("CI") == "true":
-        pca_filenames = ["PCA Info.xlsx", "PCA Feature Summary.xlsx"]
-    else:
-        pca_filenames = [
-            "PCA Feature Summary.xlsx",
-            "PCA ID Info.xlsx",
-            "PCA Info.xlsx",
-        ]
-    for filename in pca_filenames:
-        true_pca_df = pd.read_excel(os.path.join(extract_true_dir, filename))
-        test_pca_df = pd.read_excel(
-            os.path.join(extract_folderinfo["results_dir"], filename)
-        )
-        pdt.assert_frame_equal(test_pca_df, true_pca_df)
-
-    # ...................  4) TEST EQUIVALENCE OF STATS.TXT & DFs  .....................
-    shallow = False  # if True compares only the metadata, not the contents!
-    match, _, _ = filecmp.cmpfiles(  # Summary Stats.txt file
-        extract_true_dir,
-        extract_folderinfo["results_dir"],
-        [STATS_TXT_FILENAME],
-        shallow,
-    )
-    assert match == [STATS_TXT_FILENAME]
-    for version_number in ["1", "2"]:  # Two Tukeys Results Excel Files
-        filename = f"Stats Multiple Comparison - Version {version_number}.xlsx"
-        true_stats_df = pd.read_excel(os.path.join(extract_true_dir, filename))
-        test_stats_df = pd.read_excel(
-            os.path.join(extract_folderinfo["results_dir"], filename)
-        )
-        pdt.assert_frame_equal(test_stats_df, true_stats_df)
-
-    # ......................  5) TEST EQUIVALENCE OF CONFIG.JSON  ......................
-    match, _, _ = filecmp.cmpfiles(
-        extract_true_dir,
-        extract_folderinfo["results_dir"],
-        [CONFIG_JSON_FILENAME],
-        shallow,
-    )
-    assert match == [CONFIG_JSON_FILENAME]