sensospot_parser/tests/test_sensovation_data_parser.py

""" Stub file for testing the project """

from pathlib import Path

import numpy
import pytest

EXAMPLE_DIR_WO_PARAMS = "mtp_wo_parameters"
EXAMPLE_DIR_WITH_PARAMS = "mtp_with_parameters"


@pytest.fixture
def example_dir(request):
    root_dir = Path(request.config.rootdir)
    yield root_dir / "example_data"


@pytest.fixture
def example_file(example_dir):
    data_dir = example_dir / EXAMPLE_DIR_WO_PARAMS
    yield data_dir / "160210_SG2-010-001_Regen_cy3100_1_A1_1.csv"


@pytest.mark.parametrize(
    "sub_dir,file_name",
    [
        (
            EXAMPLE_DIR_WO_PARAMS,
            "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv",
        ),
        (
            EXAMPLE_DIR_WITH_PARAMS,
            "160210_SG2-010-001_Regen_cy3100_1_A1_1.csv",
        ),
    ],
)
def test_parse_csv(example_dir, sub_dir, file_name):
    from sensovation_data_parser import _parse_csv

    result = _parse_csv(example_dir / sub_dir / file_name)

    columns = {
        " ID ": numpy.int64,
        "Pos.X": numpy.int64,
        "Pos.Y": numpy.int64,
        "Bkg.Mean": float,
        "Spot.Mean": float,
        "Bkg.Median": float,
        "Spot.Median": float,
        "Bkg.StdDev": float,
        "Spot.StdDev": float,
        "Bkg.Sum": numpy.int64,
        "Spot.Sum": numpy.int64,
        "Bkg.Area": numpy.int64,
        "Spot.Area": numpy.int64,
        "Spot.Sat. (%)": numpy.int64,
        "Found": numpy.bool_,
        "Pos.Nom.X": numpy.int64,
        "Pos.Nom.Y": numpy.int64,
        "Dia.": numpy.int64,
        "Rect.": str,
        "Contour": object,  # ignore the type of contour
    }

    assert set(result.columns) == set(columns.keys())
    assert len(result[" ID "].unique()) == 100
    assert len(result) == 100
    for column, value_type in columns.items():
        assert isinstance(result[column][0], value_type)


@pytest.mark.parametrize(
    "input,expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", "."),]
)
def test_guess_decimal_separator_returns_correct_separator(input, expected):
    from sensovation_data_parser import _guess_decimal_separator
    from io import StringIO

    handle = StringIO(f"header\n{input}\n")
    result = _guess_decimal_separator(handle)

    assert result == expected


def test_guess_decimal_separator_rewinds_handle():
    from sensovation_data_parser import _guess_decimal_separator
    from io import StringIO

    handle = StringIO(f"header\n{input}\n")
    _guess_decimal_separator(handle)

    assert next(handle) == "header\n"