data/tests/conftest.py

"""
Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
License: GNU GPL 2.0
"""

# flake8: noqa
# Pre-configuration to add the OpenSlide DLL directory to the system's environment variables
import os
import sys


def configure_openslide_path():
    print("Configuring OpenSlide path on", sys.platform)

    # Check if the os.add_dll_directory function is available (Python 3.8+ on Windows)
    if hasattr(os, "add_dll_directory"):
        openslide_path = os.getenv("OPENSLIDE_PATH")
        if openslide_path:
            print("Adding OpenSlide path:", openslide_path)
            os.add_dll_directory(openslide_path)
        else:
            raise RuntimeError(
                "OPENSLIDE_PATH environment variable is not set or incorrect."
            )
    else:
        print(
            "os.add_dll_directory not available, ensure your Python version is 3.8 or higher on Windows"
        )


# Call the pre-configuration function before importing OpenSlide
configure_openslide_path()

import cv2
import javabridge
import numpy as np
import openslide
import pytest
import scanpy as sc

from pathml.core import Tile, VectraSlide, types


def pytest_sessionfinish(session, exitstatus):
    """
    Pytest will not terminate if javabridge is not killed.
    But if we terminate javabridge in BioFormatsBackend, we can not spawn another javabridge in the same thread.

    This Pytest sessionfinish hook runs automatically at the end of testing.
    """
    javabridge.kill_vm()


@pytest.fixture(autouse=True)
def remove_duplicate_paths():
    yield  # Wait for the test to finish
    # Split the PATH by the OS-specific path separator
    paths = os.environ["PATH"].split(os.pathsep)
    # Remove duplicates while preserving order
    unique_paths = list(dict.fromkeys(paths))
    # Join the unique paths back into a string and set it as the new PATH
    os.environ["PATH"] = os.pathsep.join(unique_paths)


def create_HE_tile():
    import openslide

    s = openslide.open_slide("tests/testdata/small_HE.svs")
    im_image = s.read_region(level=0, location=(900, 800), size=(500, 500))
    im_np = np.asarray(im_image)
    im_np_rgb = cv2.cvtColor(im_np, cv2.COLOR_RGBA2RGB)
    # make mask object
    masks = np.random.randint(
        low=1, high=255, size=(im_np_rgb.shape[0], im_np_rgb.shape[1]), dtype=np.uint8
    )
    masks = {"testmask": masks}
    # labels dict
    labs = {
        "test_string_label": "testlabel",
        "test_array_label": np.array([2, 3, 4]),
        "test_int_label": 3,
        "test_float_label": 3.0,
        "test_bool_label": True,
    }
    tile = Tile(image=im_np_rgb, coords=(1, 3), masks=masks, labels=labs)
    return tile


@pytest.fixture
def tile():
    """
    Example of pathml.core.Tile object, with no slide_type
    """
    tile = create_HE_tile()
    return tile


@pytest.fixture
def tileHE():
    """
    Example of pathml.core.Tile object, of type HE
    """
    tile = create_HE_tile()
    tile.slide_type = types.HE
    return tile


@pytest.fixture
def tileVectra():
    """
    Example of pathml.core.Tile representation of Vectra image
    """
    slidedata = VectraSlide("tests/testdata/small_vectra.qptiff", backend="bioformats")
    region = slidedata.slide.extract_region(location=(0, 0), size=(256, 256))

    # make mask object
    masks = np.random.randint(
        low=1, high=255, size=(region.shape[0], region.shape[1]), dtype=np.uint8
    )
    masks = {"testmask": masks}

    # labels dict
    labs = {
        "test_string_label": "testlabel",
        "test_array_label": np.array([2, 3, 4]),
        "test_int_label": 3,
        "test_float_label": 3.0,
        "test_bool_label": True,
    }

    tile = Tile(
        image=region, coords=(0, 0), masks=masks, slide_type=types.Vectra, labels=labs
    )
    return tile


@pytest.fixture
def anndata():
    """
    Example anndata.AnnData object
    """
    adata = sc.datasets.pbmc3k_processed()
    return adata


@pytest.fixture
def tileCODEX():
    """
    Example of pathml.core.Tile representation of CODEX image.
    """
    # Set dimensions for the mock CODEX image
    x_dim, y_dim, z_dim, c_dim, t_dim = 100, 100, 3, 4, 5  # Example dimensions

    # Create a mock CODEX image
    codex_image = np.random.rand(x_dim, y_dim, z_dim, c_dim, t_dim)

    # Create and return a Tile object
    tile = Tile(
        image=codex_image,
        coords=(0, 0),
        slide_type=types.CODEX,  # Assuming 'CODEX' is a valid type
        # Additional properties like masks and labels can be added as needed
    )
    return tile