nimare 0.4.2rc4__py3-none-any.whl

nimare/tests/conftest.py

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+"""Generate fixtures for tests."""
+
+import json
+import os
+from shutil import copyfile
+
+import nibabel as nib
+import numpy as np
+import pytest
+from nilearn.image import resample_img
+from requests import request
+
+import nimare
+from nimare.generate import create_coordinate_dataset
+from nimare.tests.utils import get_test_data_path
+from nimare.utils import get_resource_path
+
+# Only enable the following once in a while for a check for SettingWithCopyWarnings
+# pd.options.mode.chained_assignment = "raise"
+
+
+@pytest.fixture(scope="session")
+def testdata_ibma(tmp_path_factory):
+    """Load data from dataset into global variables."""
+    tmpdir = tmp_path_factory.mktemp("testdata_ibma")
+
+    # Load dataset
+    dset_file = os.path.join(get_test_data_path(), "test_pain_dataset.json")
+    dset_dir = os.path.join(get_test_data_path(), "test_pain_dataset")
+    mask_file = os.path.join(dset_dir, "mask.nii.gz")
+    dset = nimare.dataset.Dataset(dset_file, mask=mask_file)
+    dset.update_path(dset_dir)
+    # Move image contents of Dataset to temporary directory
+    for c in dset.images.columns:
+        if c.endswith("__relative"):
+            continue
+        for f in dset.images[c].values:
+            if (f is None) or not os.path.isfile(f):
+                continue
+            new_f = f.replace(
+                dset_dir.rstrip(os.path.sep), str(tmpdir.absolute()).rstrip(os.path.sep)
+            )
+            dirname = os.path.dirname(new_f)
+            if not os.path.isdir(dirname):
+                os.makedirs(dirname)
+            copyfile(f, new_f)
+    dset.update_path(tmpdir)
+    return dset
+
+
+@pytest.fixture(scope="session")
+def testdata_cbma():
+    """Generate coordinate-based dataset for tests."""
+    dset_file = os.path.join(get_test_data_path(), "test_pain_dataset.json")
+    dset = nimare.dataset.Dataset(dset_file)
+
+    # Only retain one peak in each study in coordinates
+    # Otherwise centers of mass will be obscured in kernel tests by overlapping
+    # kernels
+    dset.coordinates = dset.coordinates.drop_duplicates(subset=["id"])
+    return dset
+
+
+@pytest.fixture(scope="session")
+def testdata_cbma_full():
+    """Generate more complete coordinate-based dataset for tests.
+
+    Same as above, except returns all coords, not just one per study.
+    """
+    dset_file = os.path.join(get_test_data_path(), "test_pain_dataset.json")
+    dset = nimare.dataset.Dataset(dset_file)
+    return dset
+
+
+@pytest.fixture(scope="session")
+def testdata_cbmr_simulated():
+    """Simulate coordinate-based dataset for tests."""
+    # simulate
+    ground_truth_foci, dset = create_coordinate_dataset(
+        foci=10, sample_size=(20, 40), n_studies=1000, seed=100
+    )
+    # set up group columns: diagnosis & drug_status
+    n_rows = dset.annotations.shape[0]
+    dset.annotations["diagnosis"] = [
+        "schizophrenia" if i % 2 == 0 else "depression" for i in range(n_rows)
+    ]
+    dset.annotations["drug_status"] = ["Yes" if i % 2 == 0 else "No" for i in range(n_rows)]
+    dset.annotations["drug_status"] = (
+        dset.annotations["drug_status"].sample(frac=1).reset_index(drop=True)
+    )  # random shuffle drug_status column
+    # set up moderators: sample sizes & avg_age
+    dset.annotations["sample_sizes"] = [dset.metadata.sample_sizes[i][0] for i in range(n_rows)]
+    dset.annotations["avg_age"] = np.arange(n_rows)
+    dset.annotations["schizophrenia_subtype"] = [
+        "type1",
+        "type2",
+        "type3",
+        "type4",
+        "type5",
+    ] * int(n_rows / 5)
+    dset.annotations["schizophrenia_subtype"] = (
+        dset.annotations["schizophrenia_subtype"].sample(frac=1).reset_index(drop=True)
+    )  # random shuffle drug_status column
+
+    return dset
+
+
+@pytest.fixture(scope="session")
+def testdata_laird():
+    """Load data from dataset into global variables."""
+    testdata_laird = nimare.dataset.Dataset(
+        os.path.join(get_test_data_path(), "neurosynth_laird_studies.json")
+    )
+    return testdata_laird
+
+
+@pytest.fixture(scope="session")
+def mni_mask():
+    """Load MNI mask for testing."""
+    return nib.load(
+        os.path.join(get_resource_path(), "templates", "MNI152_2x2x2_brainmask.nii.gz")
+    )
+
+
+@pytest.fixture(scope="session")
+def roi_img():
+    """Load MNI mask for testing."""
+    return nib.load(os.path.join(get_test_data_path(), "amygdala_roi.nii.gz"))
+
+
+@pytest.fixture(scope="session")
+def testdata_ibma_resample(tmp_path_factory):
+    """Create dataset for image-based resampling tests."""
+    tmpdir = tmp_path_factory.mktemp("testdata_ibma_resample")
+
+    # Load dataset
+    dset_file = os.path.join(get_test_data_path(), "test_pain_dataset.json")
+    dset_dir = os.path.join(get_test_data_path(), "test_pain_dataset")
+    mask_file = os.path.join(dset_dir, "mask.nii.gz")
+    dset = nimare.dataset.Dataset(dset_file, mask=mask_file)
+    dset.update_path(dset_dir)
+
+    # create reproducible random number generator for resampling
+    rng = np.random.default_rng(seed=123)
+    # Move image contents of Dataset to temporary directory
+    for c in dset.images.columns:
+        if c.endswith("__relative"):
+            continue
+
+        for f in dset.images[c].values:
+            if (f is None) or not os.path.isfile(f):
+                continue
+
+            new_f = f.replace(
+                dset_dir.rstrip(os.path.sep), str(tmpdir.absolute()).rstrip(os.path.sep)
+            )
+            dirname = os.path.dirname(new_f)
+            if not os.path.isdir(dirname):
+                os.makedirs(dirname)
+
+            # create random affine to make images different shapes
+            affine = np.eye(3)
+            np.fill_diagonal(affine, rng.choice([1, 2, 3]))
+            img = resample_img(
+                nib.load(f),
+                target_affine=affine,
+                interpolation="linear",
+                clip=True,
+            )
+            nib.save(img, new_f)
+    dset.update_path(tmpdir)
+    return dset
+
+
+@pytest.fixture(scope="session")
+def example_nimads_studyset():
+    """Download/lookup example NiMADS studyset."""
+    out_file = os.path.join(get_test_data_path(), "nimads_studyset.json")
+    if not os.path.isfile(out_file):
+        url = "https://neurostore.org/api/studysets/Cv2LLUqG76W9?nested=true"
+        response = request("GET", url)
+        with open(out_file, "wb") as f:
+            f.write(response.content)
+    with open(out_file, "r") as f:
+        studyset = json.load(f)
+    return studyset
+
+
+@pytest.fixture(scope="session")
+def example_nimads_annotation():
+    """Download/lookup example NiMADS annotation."""
+    out_file = os.path.join(get_test_data_path(), "nimads_annotation.json")
+    if not os.path.isfile(out_file):
+        url = "https://neurostore.org/api/annotations/76PyNqoTNEsE"
+        response = request("GET", url)
+        with open(out_file, "wb") as f:
+            f.write(response.content)
+    with open(out_file, "r") as f:
+        annotation = json.load(f)
+    return annotation
+
+
+@pytest.fixture(scope="session")
+def testdata_ibma_multiple_contrasts(tmp_path_factory):
+    """Load data from dataset into global variables."""
+    tmpdir = tmp_path_factory.mktemp("testdata_ibma_multiple_contrasts")
+
+    # Load dataset
+    dset_file = os.path.join(get_test_data_path(), "test_pain_dataset_multiple_contrasts.json")
+    dset_dir = os.path.join(get_test_data_path(), "test_pain_dataset")
+    mask_file = os.path.join(dset_dir, "mask.nii.gz")
+    dset = nimare.dataset.Dataset(dset_file, mask=mask_file)
+    dset.update_path(dset_dir)
+    # Move image contents of Dataset to temporary directory
+    for c in dset.images.columns:
+        if c.endswith("__relative"):
+            continue
+        for f in dset.images[c].values:
+            if (f is None) or not os.path.isfile(f):
+                continue
+            new_f = f.replace(
+                dset_dir.rstrip(os.path.sep), str(tmpdir.absolute()).rstrip(os.path.sep)
+            )
+            dirname = os.path.dirname(new_f)
+            if not os.path.isdir(dirname):
+                os.makedirs(dirname)
+            copyfile(f, new_f)
+    dset.update_path(tmpdir)
+    return dset

nimare/tests/data/data-neurosynth_version-7_vocab-terms_vocabulary.txt

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+001
+01
+05
+10
+100
+11
+12
+12 healthy
+13
+14
+14 healthy
+15
+15 healthy
+16
+16 healthy
+17
+18
+18 healthy
+19
+20
+20 healthy
+200
+2014
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+3d
+3t
+40
+41
+42
+43
+44
+45
+46
+47
+48
+49
+50
+60
+70
+75
+80
+90
+aberrant
+abilities
+ability
+able
+abnormal
+abnormalities
+abnormality
+absence
+absent
+abstract
+abuse
+acc
+access
+accompanied
+accordance
+according
+accordingly
+account
+accounted
+accounts
+accumbens
+accuracy
+accurate
+accurately
+achieve
+achieved
+acoustic
+acquired
+acquisition
+act
+action
+action observation
+actions
+activate
+activates
+activations
+active
+actively
+activities
+acts