nimare 0.4.2rc4__py3-none-any.whl

nimare/io.py

@@ -0,0 +1,635 @@
+"""Input/Output operations."""
+
+import json
+import logging
+import re
+from collections import Counter
+from itertools import groupby
+from operator import itemgetter
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import requests
+from scipy import sparse
+
+from nimare.dataset import Dataset
+from nimare.extract.utils import _get_dataset_dir
+from nimare.utils import _create_name, load_nimads
+
+LGR = logging.getLogger(__name__)
+
+DEFAULT_MAP_TYPE_CONVERSION = {
+    "T map": "t",
+    "variance": "varcope",
+    "univariate-beta map": "beta",
+    "Z map": "z",
+    "p map": "p",
+}
+
+
+def convert_nimads_to_dataset(studyset, annotation=None):
+    """Convert nimads studyset to a dataset.
+
+    .. versionadded:: 0.0.14
+
+    Parameters
+    ----------
+    studyset : :obj:`str`, :obj:`dict`, :obj:`nimare.nimads.StudySet`
+        Path to a JSON file containing a nimads studyset, a dictionary containing a nimads
+        studyset, or a nimads studyset object.
+    annotation : :obj:`str`, :obj:`dict`, :obj:`nimare.nimads.Annotation`, optional
+        Optional path to a JSON file containing a nimads annotation, a dictionary containing a
+        nimads annotation, or a nimads annotation object.
+
+    Returns
+    -------
+    dset : :obj:`nimare.dataset.Dataset`
+        NiMARE Dataset object containing experiment information from nimads studyset.
+    """
+
+    def _analysis_to_dict(study, analysis):
+        result = {
+            "metadata": {
+                "authors": study.name,
+                "journal": study.publication,
+                "title": study.name,
+            },
+            "coords": {
+                "space": analysis.points[0].space if analysis.points else "UNKNOWN",
+                "x": [p.x for p in analysis.points] or [None],
+                "y": [p.y for p in analysis.points] or [None],
+                "z": [p.z for p in analysis.points] or [None],
+            },
+        }
+        sample_size = study.metadata.get("sample_size")
+        if sample_size:
+            result["metadata"]["sample_sizes"] = [sample_size]
+        if analysis.annotations:
+            result["labels"] = {}
+            for annotation in analysis.annotations.values():
+                result["labels"].update(annotation)
+
+        return result
+
+    def _study_to_dict(study):
+        return {
+            "metadata": {
+                "authors": study.authors,
+                "journal": study.publication,
+                "title": study.name,
+            },
+            "contrasts": {_create_name(a): _analysis_to_dict(study, a) for a in study.analyses},
+        }
+
+    # load nimads studyset
+    studyset = load_nimads(studyset, annotation)
+    return Dataset({_create_name(s): _study_to_dict(s) for s in list(studyset.studies)})
+
+
+def convert_neurosynth_to_dict(
+    coordinates_file,
+    metadata_file,
+    annotations_files=None,
+    feature_groups=None,
+):
+    """Convert Neurosynth/NeuroQuery database files to a dictionary.
+
+    .. versionchanged:: 0.0.10
+
+        * Use new format for Neurosynth and NeuroQuery files.
+
+    .. versionchanged:: 0.0.9
+
+        * Support annotations files organized in a dictionary.
+
+    Parameters
+    ----------
+    coordinates_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's coordinates.
+    metadata_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's metadata.
+    annotations_files : :obj:`dict`, :obj:`list` of :obj:`dict`, or None, optional
+        Optional file(s) with Neurosynth/NeuroQuery's annotations.
+        This should consist of a dictionary with two keys: "features" and "vocabulary".
+        "features" should have an NPZ file containing a sparse matrix of feature values.
+        "vocabulary" should have a TXT file containing labels.
+        The vocabulary corresponds to the columns of the feature matrix, while study IDs are
+        inferred from the metadata file, which MUST be in the same order as the features matrix.
+        Multiple sets of annotations may be provided, in which case "annotations_files" should be
+        a list of dictionaries. The appropriate name of each annotation set will be inferred from
+        the "features" filename, but this can be overwritten by using the "feature_groups"
+        parameter.
+        Default is None.
+    feature_groups : :obj:`list` of :obj:`str`, or None, optional
+        An optional list of names of annotation sets defined in "annotations_files".
+        This should only be used if "annotations_files" is used and the users wants to override
+        the automatically-extracted annotation set names.
+        Default is None.
+
+    Returns
+    -------
+    dset_dict : :obj:`dict`
+        NiMARE-organized dictionary containing experiment information from text files.
+
+    Warnings
+    --------
+    Starting in version 0.0.10, this function operates on the new Neurosynth/NeuroQuery file
+    format. Old code using this function **will not work** with the new version.
+    """
+    coords_df = pd.read_table(coordinates_file)
+    metadata_df = pd.read_table(metadata_file)
+    assert metadata_df["id"].is_unique, "Metadata file must have one row per ID."
+
+    coords_df["id"] = coords_df["id"].astype(str)
+    metadata_df["id"] = metadata_df["id"].astype(str)
+    metadata_df = metadata_df.set_index("id", drop=False)
+    ids = metadata_df["id"].tolist()
+
+    if "space" not in metadata_df.columns:
+        LGR.warning("No 'space' column detected. Defaulting to 'UNKNOWN'.")
+        metadata_df["space"] = "UNKNOWN"
+
+    if isinstance(annotations_files, dict):
+        annotations_files = [annotations_files]
+
+    if isinstance(feature_groups, str):
+        feature_groups = [feature_groups]
+
+    # Load labels into a single DataFrame
+    if annotations_files is not None:
+        label_dfs = []
+        if feature_groups is not None:
+            assert len(feature_groups) == len(annotations_files)
+
+        for i_feature_group, annotations_dict in enumerate(annotations_files):
+            features_file = annotations_dict["features"]
+            vocabulary_file = annotations_dict["vocabulary"]
+
+            vocab = re.findall("vocab-([a-zA-Z0-9]+)_", features_file)[0]
+            source = re.findall("source-([a-zA-Z0-9]+)_", features_file)[0]
+            value_type = re.findall("type-([a-zA-Z0-9]+)_", features_file)[0]
+
+            if feature_groups is not None:
+                feature_group = feature_groups[i_feature_group]
+                feature_group = feature_group.rstrip("_") + "__"
+            else:
+                feature_group = f"{vocab}_{source}_{value_type}__"
+
+            features = sparse.load_npz(features_file).todense()
+            vocab = np.loadtxt(vocabulary_file, dtype=str, delimiter="\t")
+
+            labels = [feature_group + label for label in vocab]
+
+            temp_label_df = pd.DataFrame(features, index=ids, columns=labels)
+            temp_label_df.index.name = "study_id"
+
+            label_dfs.append(temp_label_df)
+
+        label_df = pd.concat(label_dfs, axis=1)
+    else:
+        label_df = None
+
+    # Compile (pseudo-)NIMADS-format dictionary
+    x = coords_df["x"].values
+    y = coords_df["y"].values
+    z = coords_df["z"].values
+
+    dset_dict = {}
+
+    for sid, study_metadata in metadata_df.iterrows():
+        coord_inds = np.where(coords_df["id"].values == sid)[0]
+        study_dict = {}
+        study_dict["metadata"] = {}
+        study_dict["metadata"]["authors"] = study_metadata.get("authors", "n/a")
+        study_dict["metadata"]["journal"] = study_metadata.get("journal", "n/a")
+        study_dict["metadata"]["year"] = study_metadata.get("year", "n/a")
+        study_dict["metadata"]["title"] = study_metadata.get("title", "n/a")
+        study_dict["contrasts"] = {}
+        study_dict["contrasts"]["1"] = {}
+        # Duplicate metadata across study and contrast levels
+        study_dict["contrasts"]["1"]["metadata"] = {}
+        study_dict["contrasts"]["1"]["metadata"]["authors"] = study_metadata.get("authors", "n/a")
+        study_dict["contrasts"]["1"]["metadata"]["journal"] = study_metadata.get("journal", "n/a")
+        study_dict["contrasts"]["1"]["metadata"]["year"] = study_metadata.get("year", "n/a")
+        study_dict["contrasts"]["1"]["metadata"]["title"] = study_metadata.get("title", "n/a")
+        study_dict["contrasts"]["1"]["coords"] = {}
+        study_dict["contrasts"]["1"]["coords"]["space"] = study_metadata["space"]
+        study_dict["contrasts"]["1"]["coords"]["x"] = list(x[coord_inds])
+        study_dict["contrasts"]["1"]["coords"]["y"] = list(y[coord_inds])
+        study_dict["contrasts"]["1"]["coords"]["z"] = list(z[coord_inds])
+
+        if label_df is not None:
+            study_dict["contrasts"]["1"]["labels"] = label_df.loc[sid].to_dict()
+
+        dset_dict[sid] = study_dict
+
+    return dset_dict
+
+
+def convert_neurosynth_to_json(
+    coordinates_file,
+    metadata_file,
+    out_file,
+    annotations_files=None,
+    feature_groups=None,
+):
+    """Convert Neurosynth/NeuroQuery dataset text file to a NiMARE json file.
+
+    .. versionchanged:: 0.0.10
+
+        * Use new format for Neurosynth and NeuroQuery files.
+
+    .. versionchanged:: 0.0.9
+
+        * Support annotations files organized in a dictionary.
+
+    Parameters
+    ----------
+    coordinates_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's coordinates and metadata.
+    metadata_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's metadata.
+    out_file : :obj:`str`
+        Output NiMARE-format json file.
+    annotations_files : :obj:`dict`, :obj:`list` of :obj:`dict`, or None, optional
+        Optional file(s) with Neurosynth/NeuroQuery's annotations.
+        This should consist of a dictionary with two keys: "features" and "vocabulary".
+        "features" should have an NPZ file containing a sparse matrix of feature values.
+        "vocabulary" should have a TXT file containing labels.
+        The vocabulary corresponds to the columns of the feature matrix, while study IDs are
+        inferred from the metadata file, which MUST be in the same order as the features matrix.
+        Multiple sets of annotations may be provided, in which case "annotations_files" should be
+        a list of dictionaries. The appropriate name of each annotation set will be inferred from
+        the "features" filename, but this can be overwritten by using the "feature_groups"
+        parameter.
+        Default is None.
+    feature_groups : :obj:`list` of :obj:`str`, or None, optional
+        An optional list of names of annotation sets defined in "annotations_files".
+        This should only be used if "annotations_files" is used and the users wants to override
+        the automatically-extracted annotation set names.
+        Default is None.
+
+    Warnings
+    --------
+    Starting in version 0.0.10, this function operates on the new Neurosynth/NeuroQuery file
+    format. Old code using this function **will not work** with the new version.
+    """
+    dset_dict = convert_neurosynth_to_dict(
+        coordinates_file, metadata_file, annotations_files, feature_groups
+    )
+    with open(out_file, "w") as fo:
+        json.dump(dset_dict, fo, indent=4, sort_keys=True)
+
+
+def convert_neurosynth_to_dataset(
+    coordinates_file,
+    metadata_file,
+    annotations_files=None,
+    feature_groups=None,
+    target="mni152_2mm",
+):
+    """Convert Neurosynth/NeuroQuery database files into NiMARE Dataset.
+
+    .. versionchanged:: 0.0.10
+
+        * Use new format for Neurosynth and NeuroQuery files.
+
+    .. versionchanged:: 0.0.9
+
+        * Support annotations files organized in a dictionary.
+
+    Parameters
+    ----------
+    coordinates_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's coordinates and metadata.
+    metadata_file : :obj:`str`
+        TSV.GZ file with Neurosynth/NeuroQuery's metadata.
+    annotations_files : :obj:`dict`, :obj:`list` of :obj:`dict`, or None, optional
+        Optional file(s) with Neurosynth/NeuroQuery's annotations.
+        This should consist of a dictionary with two keys: "features" and "vocabulary".
+        "features" should have an NPZ file containing a sparse matrix of feature values.
+        "vocabulary" should have a TXT file containing labels.
+        The vocabulary corresponds to the columns of the feature matrix, while study IDs are
+        inferred from the metadata file, which MUST be in the same order as the features matrix.
+        Multiple sets of annotations may be provided, in which case "annotations_files" should be
+        a list of dictionaries. The appropriate name of each annotation set will be inferred from
+        the "features" filename, but this can be overwritten by using the "feature_groups"
+        parameter.
+        Default is None.
+    feature_groups : :obj:`list` of :obj:`str`, or None, optional
+        An optional list of names of annotation sets defined in "annotations_files".
+        This should only be used if "annotations_files" is used and the users wants to override
+        the automatically-extracted annotation set names.
+        Default is None.
+    target : {'mni152_2mm', 'ale_2mm'}, optional
+        Target template space for coordinates. Default is 'mni152_2mm'.
+
+    Returns
+    -------
+    :obj:`~nimare.dataset.Dataset`
+        Dataset object containing experiment information from text_file.
+
+    Warnings
+    --------
+    Starting in version 0.0.10, this function operates on the new Neurosynth/NeuroQuery file
+    format. Old code using this function **will not work** with the new version.
+    """
+    dset_dict = convert_neurosynth_to_dict(
+        coordinates_file,
+        metadata_file,
+        annotations_files,
+        feature_groups,
+    )
+    return Dataset(dset_dict, target=target)
+
+
+def convert_sleuth_to_dict(text_file):
+    """Convert Sleuth text file to a dictionary.
+
+    Parameters
+    ----------
+    text_file : :obj:`str` or :obj:`list` of :obj:`str`
+        Path to Sleuth-format text file.
+        More than one text file may be provided.
+
+    Returns
+    -------
+    :obj:`dict`
+        NiMARE-organized dictionary containing experiment information from text file.
+    """
+    if isinstance(text_file, list):
+        dset_dict = {}
+        for tf in text_file:
+            temp_dict = convert_sleuth_to_dict(tf)
+            for sid in temp_dict.keys():
+                if sid in dset_dict.keys():
+                    dset_dict[sid]["contrasts"] = {
+                        **dset_dict[sid]["contrasts"],
+                        **temp_dict[sid]["contrasts"],
+                    }
+                else:
+                    dset_dict[sid] = temp_dict[sid]
+        return dset_dict
+
+    with open(text_file, "r") as file_object:
+        data = file_object.read()
+
+    data = [line.rstrip() for line in re.split("\n\r|\r\n|\n|\r", data)]
+    data = [line for line in data if line]
+    # First line indicates space. The rest are studies, ns, and coords
+    space = data[0].replace(" ", "").replace("//Reference=", "")
+
+    SPACE_OPTS = ["MNI", "TAL", "Talairach"]
+    if space not in SPACE_OPTS:
+        raise ValueError(f"Space {space} unknown. Options supported: {', '.join(SPACE_OPTS)}.")
+
+    # Split into experiments
+    data = data[1:]
+    exp_idx = []
+    header_lines = [i for i in range(len(data)) if data[i].startswith("//")]
+
+    # Get contiguous header lines to define contrasts
+    ranges = []
+    for k, g in groupby(enumerate(header_lines), lambda x: x[0] - x[1]):
+        group = list(map(itemgetter(1), g))
+        ranges.append((group[0], group[-1]))
+        if "Subjects" not in data[group[-1]]:
+            raise ValueError(f"Sample size line missing for {data[group[0] : group[-1] + 1]}")
+    start_idx = [r[0] for r in ranges]
+    end_idx = start_idx[1:] + [len(data) + 1]
+    split_idx = zip(start_idx, end_idx)
+
+    dset_dict = {}
+    for i_exp, exp_idx in enumerate(split_idx):
+        exp_data = data[exp_idx[0] : exp_idx[1]]
+        if exp_data:
+            header_idx = [i for i in range(len(exp_data)) if exp_data[i].startswith("//")]
+            study_info_idx = header_idx[:-1]
+            n_idx = header_idx[-1]
+            study_info = [exp_data[i].replace("//", "").strip() for i in study_info_idx]
+            study_info = " ".join(study_info)
+            study_name = study_info.split(":")[0]
+            contrast_name = ":".join(study_info.split(":")[1:]).strip()
+            sample_size = int(exp_data[n_idx].replace(" ", "").replace("//Subjects=", ""))
+            xyz = exp_data[n_idx + 1 :]  # Coords are everything after study info and n
+            xyz = [row.split() for row in xyz]
+            correct_shape = np.all([len(coord) == 3 for coord in xyz])
+            if not correct_shape:
+                all_shapes = np.unique([len(coord) for coord in xyz]).astype(str)
+                raise ValueError(
+                    f"Coordinates for study '{study_info}' are not all "
+                    f"correct length. Lengths detected: {', '.join(all_shapes)}."
+                )
+
+            try:
+                xyz = np.array(xyz, dtype=float)
+            except:
+                # Prettify xyz before reporting error
+                strs = [[str(e) for e in row] for row in xyz]
+                lens = [max(map(len, col)) for col in zip(*strs)]
+                fmt = "\t".join("{{:{}}}".format(x) for x in lens)
+                table = "\n".join([fmt.format(*row) for row in strs])
+                raise ValueError(
+                    f"Conversion to numpy array failed for study '{study_info}'. Coords:\n{table}"
+                )
+
+            x, y, z = list(xyz[:, 0]), list(xyz[:, 1]), list(xyz[:, 2])
+
+            if study_name not in dset_dict.keys():
+                dset_dict[study_name] = {"contrasts": {}}
+            dset_dict[study_name]["contrasts"][contrast_name] = {"coords": {}, "metadata": {}}
+            dset_dict[study_name]["contrasts"][contrast_name]["coords"]["space"] = space
+            dset_dict[study_name]["contrasts"][contrast_name]["coords"]["x"] = x
+            dset_dict[study_name]["contrasts"][contrast_name]["coords"]["y"] = y
+            dset_dict[study_name]["contrasts"][contrast_name]["coords"]["z"] = z
+            dset_dict[study_name]["contrasts"][contrast_name]["metadata"]["sample_sizes"] = [
+                sample_size
+            ]
+    return dset_dict
+
+
+def convert_sleuth_to_json(text_file, out_file):
+    """Convert Sleuth output text file into json.
+
+    Parameters
+    ----------
+    text_file : :obj:`str` or :obj:`list` of :obj:`str`
+        Path to Sleuth-format text file.
+        More than one text file may be provided.
+    out_file : :obj:`str`
+        Path to output json file.
+    """
+    if not isinstance(text_file, str) and not isinstance(text_file, list):
+        raise ValueError(f"Unsupported type for parameter 'text_file': {type(text_file)}")
+    dset_dict = convert_sleuth_to_dict(text_file)
+
+    with open(out_file, "w") as fo:
+        json.dump(dset_dict, fo, indent=4, sort_keys=True)
+
+
+def convert_sleuth_to_dataset(text_file, target="ale_2mm"):
+    """Convert Sleuth output text file into NiMARE Dataset.
+
+    Parameters
+    ----------
+    text_file : :obj:`str` or :obj:`list` of :obj:`str`
+        Path to Sleuth-format text file.
+        More than one text file may be provided.
+    target : {'ale_2mm', 'mni152_2mm'}, optional
+        Target template space for coordinates. Default is 'ale_2mm'
+        (ALE-specific brainmask in MNI152 2mm space).
+
+    Returns
+    -------
+    :obj:`~nimare.dataset.Dataset`
+        Dataset object containing experiment information from text_file.
+    """
+    if not isinstance(text_file, str) and not isinstance(text_file, list):
+        raise ValueError(f"Unsupported type for parameter 'text_file': {type(text_file)}")
+    dset_dict = convert_sleuth_to_dict(text_file)
+    return Dataset(dset_dict, target=target)
+
+
+def convert_neurovault_to_dataset(
+    collection_ids,
+    contrasts,
+    img_dir=None,
+    map_type_conversion=None,
+    **dset_kwargs,
+):
+    """Convert a group of NeuroVault collections into a NiMARE Dataset.
+
+    .. versionadded:: 0.0.8
+
+    Parameters
+    ----------
+    collection_ids : :obj:`list` of :obj:`int` or :obj:`dict`
+        A list of collections on neurovault specified by their id.
+        The collection ids can accessed through the neurovault API
+        (i.e., https://neurovault.org/api/collections) or
+        their main website (i.e., https://neurovault.org/collections).
+        For example, in this URL https://neurovault.org/collections/8836/,
+        `8836` is the collection id.
+        collection_ids can also be a dictionary whose keys are the informative
+        study name and the values are collection ids to give the collections
+        more informative names in the dataset.
+    contrasts : :obj:`dict`
+        Dictionary whose keys represent the name of the contrast in
+        the dataset and whose values represent a regular expression that would
+        match the names represented in NeuroVault.
+        For example, under the ``Name`` column in this URL
+        https://neurovault.org/collections/8836/,
+        a valid contrast could be "as-Animal", which will be called "animal" in the created
+        dataset if the contrasts argument is ``{'animal': "as-Animal"}``.
+    img_dir : :obj:`str` or None, optional
+        Base path to save all the downloaded images, by default the images
+        will be saved to a temporary directory with the prefix "neurovault".
+    map_type_conversion : :obj:`dict` or None, optional
+        Dictionary whose keys are what you expect the `map_type` name to
+        be in neurovault and the values are the name of the respective
+        statistic map in a nimare dataset. Default = None.
+    **dset_kwargs : keyword arguments passed to Dataset
+        Keyword arguments to pass in when creating the Dataset object.
+        see :obj:`~nimare.dataset.Dataset` for details.
+
+    Returns
+    -------
+    :obj:`~nimare.dataset.Dataset`
+        Dataset object containing experiment information from neurovault.
+    """
+    img_dir = Path(_get_dataset_dir("_".join(contrasts.keys()), data_dir=img_dir))
+
+    if map_type_conversion is None:
+        map_type_conversion = DEFAULT_MAP_TYPE_CONVERSION
+
+    if not isinstance(collection_ids, dict):
+        collection_ids = {nv_coll: nv_coll for nv_coll in collection_ids}
+
+    dataset_dict = {}
+    for coll_name, nv_coll in collection_ids.items():
+        nv_url = f"https://neurovault.org/api/collections/{nv_coll}/images/?format=json"
+        images = requests.get(nv_url).json()
+        if "Not found" in images.get("detail", ""):
+            raise ValueError(
+                f"Collection {nv_coll} not found. "
+                "Three likely causes are (1) the collection doesn't exist, "
+                "(2) the collection is private, or "
+                "(3) the provided ID corresponds to an image instead of a collection."
+            )
+
+        dataset_dict[f"study-{coll_name}"] = {"contrasts": {}}
+        for contrast_name, contrast_regex in contrasts.items():
+            dataset_dict[f"study-{coll_name}"]["contrasts"][contrast_name] = {
+                "images": {
+                    "beta": None,
+                    "t": None,
+                    "varcope": None,
+                },
+                "metadata": {"sample_sizes": None},
+            }
+
+            sample_sizes = []
+            no_images = True
+            for img_dict in images["results"]:
+                if not (
+                    re.match(contrast_regex, img_dict["name"])
+                    and img_dict["map_type"] in map_type_conversion
+                    and img_dict["analysis_level"] == "group"
+                ):
+                    continue
+
+                no_images = False
+                filename = img_dir / (
+                    f"collection-{nv_coll}_id-{img_dict['id']}_" + Path(img_dict["file"]).name
+                )
+
+                if not filename.exists():
+                    r = requests.get(img_dict["file"])
+                    with open(filename, "wb") as f:
+                        f.write(r.content)
+
+                (
+                    dataset_dict[f"study-{coll_name}"]["contrasts"][contrast_name]["images"][
+                        map_type_conversion[img_dict["map_type"]]
+                    ]
+                ) = filename.as_posix()
+
+                # aggregate sample sizes (should all be the same)
+                sample_sizes.append(img_dict["number_of_subjects"])
+
+            if no_images:
+                raise ValueError(
+                    f"No images were found for contrast {contrast_name}. "
+                    f"Please check the contrast regular expression: {contrast_regex}"
+                )
+            # take modal sample size (raise warning if there are multiple values)
+            if len(set(sample_sizes)) > 1:
+                sample_size = _resolve_sample_size(sample_sizes)
+                LGR.warning(
+                    (
+                        f"Multiple sample sizes were found for neurovault collection: {nv_coll}"
+                        f"for contrast: {contrast_name}, sample sizes: {set(sample_sizes)}"
+                        f", selecting modal sample size: {sample_size}"
+                    )
+                )
+            else:
+                sample_size = sample_sizes[0]
+            (
+                dataset_dict[f"study-{coll_name}"]["contrasts"][contrast_name]["metadata"][
+                    "sample_sizes"
+                ]
+            ) = [sample_size]
+
+    dataset = Dataset(dataset_dict, **dset_kwargs)
+
+    return dataset
+
+
+def _resolve_sample_size(sample_sizes):
+    """Choose modal sample_size if there are multiple sample_sizes to choose from."""
+    sample_size_counts = Counter(sample_sizes)
+    if None in sample_size_counts:
+        sample_size_counts.pop(None)
+
+    return sample_size_counts.most_common()[0][0]

nimare/meta/__init__.py

@@ -0,0 +1,39 @@
+"""Coordinate-, image-, and effect-size-based meta-analysis estimators."""
+
+from . import ibma, kernel
+from .cbma import ALE, KDA, SCALE, ALESubtraction, MKDAChi2, MKDADensity, ale, mkda
+from .ibma import (
+    DerSimonianLaird,
+    Fishers,
+    Hedges,
+    PermutedOLS,
+    SampleSizeBasedLikelihood,
+    Stouffers,
+    VarianceBasedLikelihood,
+    WeightedLeastSquares,
+)
+from .kernel import ALEKernel, KDAKernel, MKDAKernel
+
+__all__ = [
+    "ALE",
+    "ALESubtraction",
+    "SCALE",
+    "MKDADensity",
+    "MKDAChi2",
+    "KDA",
+    "DerSimonianLaird",
+    "Fishers",
+    "Hedges",
+    "PermutedOLS",
+    "SampleSizeBasedLikelihood",
+    "Stouffers",
+    "VarianceBasedLikelihood",
+    "WeightedLeastSquares",
+    "MKDAKernel",
+    "ALEKernel",
+    "KDAKernel",
+    "kernel",
+    "ibma",
+    "ale",
+    "mkda",
+]

nimare/meta/cbma/__init__.py

@@ -0,0 +1,6 @@
+"""Coordinate-based meta-analytic estimators."""
+
+from .ale import ALE, SCALE, ALESubtraction
+from .mkda import KDA, MKDAChi2, MKDADensity
+
+__all__ = ["ALE", "ALESubtraction", "SCALE", "MKDADensity", "MKDAChi2", "KDA"]