junifer 0.0.3.dev186__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/markers/reho/tests/test_reho_estimator.py

@@ -1,260 +0,0 @@
-"""Provide tests for ReHo map compute comparison."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import time
-
-import nibabel as nib
-import pytest
-from scipy.stats import pearsonr
-
-from junifer.datareader.default import DefaultDataReader
-from junifer.markers.reho.reho_estimator import ReHoEstimator
-from junifer.pipeline.utils import _check_afni
-from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
-from junifer.utils.logging import logger
-
-
-def test_reho_estimator_cache_python() -> None:
-    """Test that the cache works properly when using Python implementation."""
-    # Get subject from datagrabber
-    with PartlyCloudyTestingDataGrabber() as dg:
-        subject = dg["sub-01"]
-    # Read data for subject
-    subject_data = DefaultDataReader().fit_transform(subject)
-    # Setup estimator
-    reho_estimator = ReHoEstimator()
-
-    first_tic = time.time()
-    reho_map_without_cache = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    first_toc = time.time()
-    logger.info(
-        f"ReHo estimator in Python without cache: {first_toc - first_tic}"
-    )
-    assert isinstance(reho_map_without_cache, nib.Nifti1Image)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 0  # no files in python
-
-    # Now fit again, should be faster
-    second_tic = time.time()
-    reho_map_with_cache = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    second_toc = time.time()
-    logger.info(
-        f"ReHo estimator in Python with cache: {second_toc - second_tic}"
-    )
-    assert isinstance(reho_map_with_cache, nib.Nifti1Image)
-    # Check that cache is being used
-    assert (second_toc - second_tic) < ((first_toc - first_tic) / 1000)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 0  # no files in python
-
-    # Now change a parameter, should compute again, without clearing the
-    # cache
-    third_tic = time.time()
-    reho_map_with_partial_cache = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=125,
-    )
-    third_toc = time.time()
-    logger.info(
-        f"ReHo estimator in Python with partial cache: {third_toc - third_tic}"
-    )
-    assert isinstance(reho_map_with_partial_cache, nib.Nifti1Image)
-    # Should require more time
-    assert (third_toc - third_tic) > ((first_toc - first_tic) / 10)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 0  # no files in python
-
-    # Now fit again with the previous params, should be fast
-    fourth_tic = time.time()
-    reho_map_with_new_cache = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=125,
-    )
-    fourth_toc = time.time()
-    logger.info(
-        f"ReHo estimator in Python with new cache: {fourth_toc - fourth_tic}"
-    )
-    assert isinstance(reho_map_with_new_cache, nib.Nifti1Image)
-    # Should require less time
-    assert (fourth_toc - fourth_tic) < ((first_toc - first_tic) / 1000)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 0  # no files in python
-
-    # Now change the data, it should clear the cache
-    with PartlyCloudyTestingDataGrabber() as dg:
-        subject = dg["sub-02"]
-    # Read data for new subject
-    subject_data = DefaultDataReader().fit_transform(subject)
-
-    fifth_tic = time.time()
-    reho_map_with_different_cache = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    fifth_toc = time.time()
-    logger.info(
-        "ReHo estimator in Python with different cache: "
-        f"{fifth_toc - fifth_tic}"
-    )
-    assert isinstance(reho_map_with_different_cache, nib.Nifti1Image)
-    # Should take less time
-    assert (fifth_toc - fifth_tic) > ((first_toc - first_tic) / 10)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 0  # no files in python
-
-
-@pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
-)
-def test_reho_estimator_cache_afni() -> None:
-    """Test that the cache works properly when using afni."""
-    # Get subject from datagrabber
-    with PartlyCloudyTestingDataGrabber() as dg:
-        subject = dg["sub-01"]
-    # Read data for subject
-    subject_data = DefaultDataReader().fit_transform(subject)
-    # Setup estimator
-    reho_estimator = ReHoEstimator()
-
-    first_tic = time.time()
-    reho_map_without_cache = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=19,
-    )
-    first_toc = time.time()
-    logger.info(
-        f"ReHo estimator in AFNI without cache: {first_toc - first_tic}"
-    )
-    assert isinstance(reho_map_without_cache, nib.Nifti1Image)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 2  # input + reho
-
-    # Now fit again, should be faster
-    second_tic = time.time()
-    reho_map_with_cache = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=19,
-    )
-    second_toc = time.time()
-    logger.info(
-        f"ReHo estimator in AFNI with cache: {second_toc - second_tic}"
-    )
-    assert isinstance(reho_map_with_cache, nib.Nifti1Image)
-    assert (second_toc - second_tic) < ((first_toc - first_tic) / 1000)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 2  # input + reho
-
-    # Now change a parameter, should compute again, without clearing the
-    # cache
-    third_tic = time.time()
-    reho_map_with_partial_cache = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    third_toc = time.time()
-    logger.info(
-        f"ReHo estimator in AFNI with partial cache: {third_toc - third_tic}"
-    )
-    assert isinstance(reho_map_with_partial_cache, nib.Nifti1Image)
-    # Should require more time
-    assert (third_toc - third_tic) > ((first_toc - first_tic) / 10)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 3  # input + 2 * reho
-
-    # Now fit again with the previous params, should be fast
-    fourth_tic = time.time()
-    reho_map_with_new_cache = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    fourth_toc = time.time()
-    logger.info(
-        f"ReHo estimator in AFNI with new cache: {fourth_toc - fourth_tic}"
-    )
-    assert isinstance(reho_map_with_new_cache, nib.Nifti1Image)
-    # Should require less time
-    assert (fourth_toc - fourth_tic) < ((first_toc - first_tic) / 1000)
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 3  # input + 2 * reho
-
-    # Now change the data, it should clear the cache
-    with PartlyCloudyTestingDataGrabber() as dg:
-        subject = dg["sub-02"]
-    # Read data for new subject
-    subject_data = DefaultDataReader().fit_transform(subject)
-
-    fifth_tic = time.time()
-    reho_map_with_different_cache = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    fifth_toc = time.time()
-    logger.info(
-        f"ReHo estimator in AFNI with different cache: {fifth_toc - fifth_tic}"
-    )
-    assert isinstance(reho_map_with_different_cache, nib.Nifti1Image)
-    # Should take less time
-    assert (fifth_toc - fifth_tic) > ((first_toc - first_tic) / 10)
-    # Count intermediate files
-    n_files = len(list(reho_estimator.temp_dir_path.glob("*")))
-    assert n_files == 2  # input + reho
-
-
-@pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
-)
-def test_reho_estimator_afni_vs_python() -> None:
-    """Compare afni and Python implementations."""
-    # Get subject from datagrabber
-    with PartlyCloudyTestingDataGrabber() as dg:
-        subject = dg["sub-01"]
-    # Read data for subject
-    subject_data = DefaultDataReader().fit_transform(subject)
-    # Setup estimator
-    reho_estimator = ReHoEstimator()
-
-    # Compare using 27 neighbours
-    reho_map_afni = reho_estimator.fit_transform(
-        use_afni=True,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-    reho_map_python = reho_estimator.fit_transform(
-        use_afni=False,
-        input_data=subject_data["BOLD"],
-        nneigh=27,
-    )
-
-    # Calculate Pearson correlation coefficient
-    r, _ = pearsonr(
-        reho_map_afni.get_fdata().flatten(),
-        reho_map_python.get_fdata().flatten(),
-    )
-    # Assert good correlation
-    assert r > 0.70

junifer-0.0.3.dev186.dist-info/RECORD

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