python-imcflibs/tests/bdv/test_define_dataset_auto.py at 72ebf118d5b1c2ac9a8671483eb03b1b37f4d93d · lguerard/python-imcflibs · GitHub

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"""Tests for the automatic dataset definition functionality in the BDV module."""

import logging

from imcflibs import pathtools
from imcflibs.imagej import bdv


def set_default_values(
    project_filename, file_path, series_type="Tiles"
):
    """Set the default values for dataset definitions.

    Parameters
    ----------
    project_filename : str
        Name of the project
    file_path : pathlib.Path
        Path to a temporary folder
    series_type : str, optional
        Type of Bioformats series (default is "Tiles")

    Returns
    -------
    str
        Start of the options for dataset definitions.
    """
    # Additional settings
    file_info = pathtools.parse_path(file_path)

    options = (
        "define_dataset=[Automatic Loader (Bioformats based)] "
        + "project_filename=["
        + project_filename
        + ".xml"
        + "] "
        + "path=["
        + file_info["path"]
        + "] "
        + "exclude=10 "
        + "bioformats_series_are?="
        + series_type
        + " "
        + "move_tiles_to_grid_(per_angle)?=[Do not move Tiles to Grid (use Metadata if available)] "
    )

    return options


def test_define_dataset_auto_tile(tmp_path, caplog):
    """Test automatic dataset definition method for tile series.

    Parameters
    ----------
    tmp_path : pytest.fixture
        Temporary path for the test.
    caplog : pytest.fixture
        Log capturing fixture.
    """

    # Set the logging level to capture warnings
    caplog.set_level(logging.WARNING)
    # Clear the log
    caplog.clear()

    # Define the project and file names
    project_filename = "proj_name"
    file_path = tmp_path
    file_info = pathtools.parse_path(file_path)

    # Define the result and dataset save paths
    result_folder = pathtools.join2(file_info["path"], project_filename)

    # Default settings

    # Define the type of Bio-Formats series
    bf_series_type = "Tiles"

    # Define the ImageJ command
    cmd = "Define Multi-View Dataset"

    # Set the default values for dataset definitions
    options = set_default_values(project_filename, file_path)

    # Construct the options for dataset definitions
    options = (
        options
        + "how_to_store_input_images=["
        + "Re-save as multiresolution HDF5"
        + "] "
        + "load_raw_data_virtually "
        + "metadata_save_path=["
        + result_folder
        + "] "
        + "image_data_save_path=["
        + result_folder
        + "] "
        + "check_stack_sizes "
        + "split_hdf5 "
        + "timepoints_per_partition=1 "
        + "setups_per_partition=0 "
        + "use_deflate_compression "
    )

    # Construct the final call to ImageJ
    final_call = "IJ.run(cmd=[%s], params=[%s])" % (cmd, options)

    # Define the dataset using the "Auto-Loader" option
    bdv.define_dataset_auto(
        project_filename, file_info["path"], bf_series_type
    )
    # Check if the final call is in the log
    assert final_call == caplog.messages[0]


def test_define_dataset_auto_angle(tmp_path, caplog):
    """Test automatic dataset definition method for angle series.

    Parameters
    ----------
    tmp_path : pytest.fixture
        Temporary path for the test.
    caplog : pytest.fixture
        Log capturing fixture.
    """

    # Set the logging level to capture warnings
    caplog.set_level(logging.WARNING)
    # Clear the log
    caplog.clear()

    # Define the project and file names
    project_filename = "proj_name"
    file_path = tmp_path
    file_info = pathtools.parse_path(file_path)

    # Define the result and dataset save paths
    result_folder = pathtools.join2(file_info["path"], project_filename)

    # Default settings

    # Define the type of Bio-Formats series
    bf_series_type = "Angles"

    # Define the ImageJ command
    cmd = "Define Multi-View Dataset"

    # Set the default values for dataset definitions
    options = set_default_values(
        project_filename, file_path, bf_series_type
    )

    # Construct the options for dataset definitions
    options = (
        options
        + "how_to_store_input_images=["
        + "Re-save as multiresolution HDF5"
        + "] "
        + "load_raw_data_virtually "
        + "metadata_save_path=["
        + result_folder
        + "] "
        + "image_data_save_path=["
        + result_folder
        + "] "
        + "check_stack_sizes "
        + "apply_angle_rotation "
        + "split_hdf5 "
        + "timepoints_per_partition=1 "
        + "setups_per_partition=0 "
        + "use_deflate_compression "
    )

    # Construct the final call to ImageJ
    final_call = "IJ.run(cmd=[%s], params=[%s])" % (cmd, options)

    # Define the dataset using the "Auto-Loader" option
    bdv.define_dataset_auto(
        project_filename, file_info["path"], bf_series_type
    )
    # Check if the final call is in the log
    assert final_call == caplog.messages[0]