test_tissuemask.py

"""Test for code related to tissue mask generation."""

import os
from pathlib import Path

import cv2
import numpy as np
import pytest
from click.testing import CliRunner

from tiatoolbox import cli
from tiatoolbox.tools import tissuemask
from tiatoolbox.utils.env_detection import running_on_ci
from tiatoolbox.wsicore import wsireader

# -------------------------------------------------------------------------------------
# Tests
# -------------------------------------------------------------------------------------


def test_otsu_masker(sample_svs: Path) -> None:
    """Test Otsu's thresholding method."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    mpp = 32
    thumb = wsi.slide_thumbnail(mpp, "mpp")
    masker = tissuemask.OtsuTissueMasker()
    mask_a = masker.fit_transform([thumb])[0]

    masker.fit([thumb])
    mask_b = masker.transform([thumb])[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_otsu_greyscale_masker(sample_svs: Path) -> None:
    """Test Otsu's thresholding method with greyscale inputs."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    mpp = 32
    thumb = wsi.slide_thumbnail(mpp, "mpp")
    thumb = cv2.cvtColor(thumb, cv2.COLOR_RGB2GRAY)
    inputs = thumb[np.newaxis, ..., np.newaxis]
    masker = tissuemask.OtsuTissueMasker()
    mask_a = masker.fit_transform(inputs)[0]

    masker.fit(inputs)
    mask_b = masker.transform(inputs)[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_morphological_masker(sample_svs: Path) -> None:
    """Test simple morphological thresholding."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    thumb = wsi.slide_thumbnail()
    masker = tissuemask.MorphologicalMasker()
    mask_a = masker.fit_transform([thumb])[0]

    masker.fit([thumb])
    mask_b = masker.transform([thumb])[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_morphological_greyscale_masker(sample_svs: Path) -> None:
    """Test morphological masker with greyscale inputs."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    mpp = 32
    thumb = wsi.slide_thumbnail(mpp, "mpp")
    thumb = cv2.cvtColor(thumb, cv2.COLOR_RGB2GRAY)
    inputs = thumb[np.newaxis, ..., np.newaxis]
    masker = tissuemask.MorphologicalMasker()
    mask_a = masker.fit_transform(inputs)[0]

    masker.fit(inputs)
    mask_b = masker.transform(inputs)[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_morphological_masker_int_kernel_size(sample_svs: Path) -> None:
    """Test simple morphological thresholding with mpp with int kernel_size."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    mpp = 32
    thumb = wsi.slide_thumbnail(mpp, "mpp")
    masker = tissuemask.MorphologicalMasker(kernel_size=5)
    mask_a = masker.fit_transform([thumb])[0]

    masker.fit([thumb])
    mask_b = masker.transform([thumb])[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_morphological_masker_mpp(sample_svs: Path) -> None:
    """Test simple morphological thresholding with mpp."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    mpp = 32
    thumb = wsi.slide_thumbnail(mpp, "mpp")
    kwarg_sets = [
        {"mpp": mpp},
        {"mpp": [mpp, mpp]},
    ]
    for kwargs in kwarg_sets:
        masker = tissuemask.MorphologicalMasker(**kwargs)
        mask_a = masker.fit_transform([thumb])[0]

        masker.fit([thumb])
        mask_b = masker.transform([thumb])[0]

        assert np.array_equal(mask_a, mask_b)
        assert masker.threshold is not None
        assert len(np.unique(mask_a)) == 2
        assert mask_a.shape == thumb.shape[:2]


def test_morphological_masker_power(sample_svs: Path) -> None:
    """Test simple morphological thresholding with objective power."""
    wsi = wsireader.OpenSlideWSIReader(sample_svs)
    power = 1.25
    thumb = wsi.slide_thumbnail(power, "power")
    masker = tissuemask.MorphologicalMasker(power=power)
    mask_a = masker.fit_transform([thumb])[0]

    masker.fit([thumb])
    mask_b = masker.transform([thumb])[0]

    assert np.array_equal(mask_a, mask_b)
    assert masker.threshold is not None
    assert len(np.unique(mask_a)) == 2
    assert mask_a.shape == thumb.shape[:2]


def test_transform_before_fit_otsu() -> None:
    """Test otsu masker error on transform before fit."""
    image = np.ones((1, 10, 10))
    masker = tissuemask.OtsuTissueMasker()
    with pytest.raises(SyntaxError, match="Fit must be called before transform."):
        masker.transform([image])[0]


def test_transform_before_fit_morphological() -> None:
    """Test morphological masker error on transform before fit."""
    image = np.ones((1, 10, 10))
    masker = tissuemask.MorphologicalMasker()
    with pytest.raises(SyntaxError, match="Fit must be called before transform."):
        masker.transform([image])[0]


def test_transform_fit_otsu_wrong_shape() -> None:
    """Test giving the incorrect input shape to otsu masker."""
    image = np.ones((10, 10))
    masker = tissuemask.OtsuTissueMasker()
    with pytest.raises(ValueError, match="Expected 4 dimensional input shape *"):
        masker.fit([image])


def test_transform_morphological_conflicting_args() -> None:
    """Test giving conflicting arguments to morphological masker."""
    with pytest.raises(
        ValueError,
        match="Only one of mpp, power, kernel_size can be given.",
    ):
        tissuemask.MorphologicalMasker(mpp=32, power=1.25)


def test_morphological_kernel_size_none() -> None:
    """Test giveing a None kernel size for morphological masker."""
    tissuemask.MorphologicalMasker(kernel_size=None)


def test_morphological_min_region_size() -> None:
    """Test morphological masker with min_region_size set.

    Creates a test image (0=foreground, 1=background) and applies the
    morphological masker with min_region_size=6. This should output
    only the largest square region as foreground in the mask
    (0=background, 1=foreground).
    """
    # Create a blank image of ones
    img = np.ones((10, 10))
    # Create a large square region of 9 zeros
    img[1:4, 1:4] = 0
    # Create a row of 5 zeros
    img[1, 5:10] = 0
    # Create a single 0
    img[8, 8] = 0

    masker = tissuemask.MorphologicalMasker(kernel_size=1, min_region_size=6)
    output = masker.fit_transform([img[..., np.newaxis]])
    assert np.sum(output[0]) == 9

    # Create the expected output with just the large square region
    # but as ones against zeros (the mask is the inverse of the input).
    expected = np.zeros((10, 10))
    expected[1:4, 1:4] = 1

    assert np.all(output[0] == expected)


@pytest.mark.skipif(running_on_ci(), reason="No display on CI.")
@pytest.mark.skipif(
    not os.environ.get("SHOW_TESTS"),
    reason="Visual tests disabled, set SHOW_TESTS to enable.",
)
def test_cli_tissue_mask_otsu_show(sample_svs: Path) -> None:
    """Test Otsu tissue masking with default input CLI and showing in a window."""
    source_img = Path(sample_svs)
    runner = CliRunner()
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Otsu",
            "--mode",
            "show",
        ],
    )

    assert tissue_mask_result.exit_code == 0


def test_cli_tissue_mask_otsu_save(sample_svs: Path) -> None:
    """Test Otsu tissue masking with default input CLI and saving to a file."""
    source_img = Path(sample_svs)
    runner = CliRunner()
    output_path = str(Path(sample_svs.parent, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Otsu",
            "--mode",
            "save",
            "--output-path",
            output_path,
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, source_img.stem + ".png").is_file()


def test_cli_tissue_mask_otsu_dir_save(sample_all_wsis: Path) -> None:
    """Test Otsu tissue masking for multiple files with default input CLI."""
    source_img = Path(sample_all_wsis)
    runner = CliRunner()
    output_path = str(Path(source_img, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Otsu",
            "--mode",
            "save",
            "--output-path",
            output_path,
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, "CMU-1-Small-Region.omnyx.png").is_file()


@pytest.mark.skipif(running_on_ci(), reason="No display on CI.")
@pytest.mark.skipif(
    not os.environ.get("SHOW_TESTS"),
    reason="Visual tests disabled, set SHOW_TESTS to enable.",
)
def test_cli_tissue_mask_morphological_show(sample_svs: Path) -> None:
    """Test Morphological tissue masking with default input CLI."""
    source_img = Path(sample_svs)
    runner = CliRunner()
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--mode",
            "show",
        ],
    )

    assert tissue_mask_result.exit_code == 0


def test_cli_tissue_mask_morphological_save(sample_svs: Path) -> None:
    """Test Morphological tissue masking with morphological method CLI."""
    source_img = Path(sample_svs)
    runner = CliRunner()
    output_path = str(Path(sample_svs.parent, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--mode",
            "save",
            "--output-path",
            output_path,
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, source_img.stem + ".png").is_file()


def test_cli_tissue_mask_morphological_power_resolution_save(sample_svs: Path) -> None:
    """Test Morphological tissue masking with morphological method CLI.

    Adds option to specify resolution and units in power (appmag).
    """
    source_img = Path(sample_svs)
    runner = CliRunner()
    output_path = str(Path(sample_svs.parent, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--mode",
            "save",
            "--output-path",
            output_path,
            "--resolution",
            1.25,
            "--units",
            "power",
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, source_img.stem + ".png").is_file()


def test_cli_tissue_mask_morphological_mpp_resolution_save(sample_svs: Path) -> None:
    """Test Morphological tissue masking with morphological method CLI.

    Adds option to specify resolution and units in mpp (micrometers per pixel).
    """
    source_img = Path(sample_svs)
    runner = CliRunner()
    output_path = str(Path(sample_svs.parent, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--mode",
            "save",
            "--output-path",
            output_path,
            "--resolution",
            32,
            "--units",
            "mpp",
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, source_img.stem + ".png").is_file()


def test_cli_tissue_mask_morphological_kernel_size_save(sample_svs: Path) -> None:
    """Test Morphological tissue masking with morphological method CLI.

    Adds option to specify kernel size.
    """
    source_img = Path(sample_svs)
    runner = CliRunner()
    output_path = str(Path(sample_svs.parent, "tissue_mask"))
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--mode",
            "save",
            "--output-path",
            output_path,
            "--kernel-size",
            "1",
            "1",
        ],
    )

    assert tissue_mask_result.exit_code == 0
    assert Path(output_path, source_img.stem + ".png").is_file()


def test_cli_tissue_mask_method_not_supported(sample_svs: Path) -> None:
    """Test method not supported for the tissue masking CLI."""
    source_img = Path(sample_svs)
    runner = CliRunner()
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Test",
            "--mode",
            "save",
        ],
    )

    assert "Invalid value for '--method'" in tissue_mask_result.output
    assert tissue_mask_result.exit_code != 0
    assert isinstance(tissue_mask_result.exception, SystemExit)

    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img),
            "--method",
            "Morphological",
            "--resolution",
            32,
            "--units",
            "level",
        ],
    )

    assert "Invalid value for '--units'" in tissue_mask_result.output
    assert tissue_mask_result.exit_code != 0
    assert isinstance(tissue_mask_result.exception, SystemExit)


def test_cli_tissue_mask_file_not_found_error(source_image: Path) -> None:
    """Test file not found error for the tissue masking CLI."""
    source_img = Path(source_image)
    runner = CliRunner()
    tissue_mask_result = runner.invoke(
        cli.main,
        [
            "tissue-mask",
            "--img-input",
            str(source_img)[:-1],
            "--method",
            "Otsu",
        ],
    )

    assert tissue_mask_result.output == ""
    assert tissue_mask_result.exit_code == 1
    assert isinstance(tissue_mask_result.exception, FileNotFoundError)