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

tests/test_common2D_unit_1_preparation.py

@@ -1,340 +0,0 @@
-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)
-    for idx in range(len(info["name"])):
-        this_info = {}
-        # forloop below is borrowed from run_singlerun_in_multirun function
-        for keyname in info.keys():
-            if "leading_" in keyname:
-                if info[keyname][idx] is not False:
-                    this_info[keyname] = info[keyname][idx]
-            else:  # pass as is for all other keys
-                this_info[keyname] = info[keyname][idx]
-    this_info["results_dir"] = tmp_path
-    # move_data... creates it, make sure it's not there
-    if os.path.exists(this_info["results_dir"]):
-        for file in os.listdir(this_info["results_dir"]):
-            os.remove(os.path.join(this_info["results_dir"], file))
-        os.rmdir(this_info["results_dir"])
-    # run with this_info
-    move_data_to_folders("DLC", ".csv", this_info, fixture_extract_folderinfo)
-    assert len(os.listdir(this_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)