brainstat 0.4.2__tar.gz → 0.5.2__tar.gz

{brainstat-0.4.2/brainstat.egg-info → brainstat-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: brainstat
-Version: 0.4.2
+Version: 0.5.2
 Summary: A toolbox for statistical analysis of neuroimaging data
 Home-page: https://github.com/MICA-LAB/BrainStat
 Author: MNI-MICA Lab and MPI-CNG Lab
@@ -13,13 +13,44 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: Topic :: Scientific/Engineering
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Requires-Python: >=3.7.*
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: abagen>=0.1
+Requires-Dist: brainspace>=0.1.2
+Requires-Dist: h5py
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: netneurotools<0.3.0
+Requires-Dist: neurosynth
+Requires-Dist: nibabel
+Requires-Dist: nilearn>=0.7.0
+Requires-Dist: nimare
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: scikit_learn>=1.0
+Requires-Dist: scipy>=1.7
+Requires-Dist: templateflow
+Requires-Dist: trimesh
+Provides-Extra: dev
+Requires-Dist: gitpython; extra == "dev"
+Requires-Dist: hcp-utils; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: plotly; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 BrainStat : A toolbox for statistical analysis of neuroimaging data
 ===================================================================

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/__init__.py

@@ -1,2 +1,2 @@
 """Neuroimaging statistics toolbox."""
-__version__ = "0.4.2"
+__version__ = "0.5.2"

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/_utils.py

@@ -150,7 +150,7 @@ def deprecated(message: str) -> Callable:
 def _download_file(
     url: str, output_file: Path, overwrite: bool = False, verbose=True
 ) -> None:
-    """Downloads a file.
+    """Downloads a file with retry logic for network failures.
 
     Parameters
     ----------
@@ -163,14 +163,39 @@ def _download_file(
     verbose : bool
         If true, print a download message, defaults to True.
     """
+    import time
+    from http.client import RemoteDisconnected
+    from urllib.error import URLError
 
     if output_file.exists() and not overwrite:
         return
 
     if verbose:
         logger.info("Downloading " + str(output_file) + " from " + url + ".")
-    with urllib.request.urlopen(url) as response, open(output_file, "wb") as out_file:
-        shutil.copyfileobj(response, out_file)
+    
+    # Retry logic for intermittent network failures
+    max_retries = 3
+    retry_delay = 2  # seconds
+    
+    for attempt in range(max_retries):
+        try:
+            with urllib.request.urlopen(url, timeout=30) as response, open(output_file, "wb") as out_file:
+                shutil.copyfileobj(response, out_file)
+            return  # Success, exit function
+        except (RemoteDisconnected, URLError, TimeoutError) as e:
+            if attempt < max_retries - 1:
+                logger.warning(
+                    f"Download attempt {attempt + 1}/{max_retries} failed: {e}. "
+                    f"Retrying in {retry_delay} seconds..."
+                )
+                time.sleep(retry_delay)
+                retry_delay *= 2  # Exponential backoff
+            else:
+                logger.error(f"Download failed after {max_retries} attempts.")
+                raise  # Re-raise the exception after all retries fail
+
+
+
 
 
 if __name__ == "__main__":

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/context/genetics.py

@@ -2,13 +2,59 @@
 import tempfile
 from pathlib import Path
 from typing import Optional, Sequence, Union
-
+import os
 import nibabel as nib
 import numpy as np
 import pandas as pd
+
+# Monkeypatch for abagen compatibility with pandas 2.0+
+if not hasattr(pd.DataFrame, 'append'):
+    def _append(self, other, ignore_index=False, verify_integrity=False, sort=False):
+        from pandas import concat
+        if isinstance(other, (list, tuple)):
+            to_concat = [self] + list(other)
+        else:
+            to_concat = [self, other]
+        return concat(to_concat, ignore_index=ignore_index, verify_integrity=verify_integrity, sort=sort)
+    pd.DataFrame.append = _append
+
+# Monkeypatch for abagen compatibility with pandas 2.0+ (set_axis inplace)
+_original_set_axis = pd.DataFrame.set_axis
+def _set_axis_patched(self, labels, *args, **kwargs):
+    if 'inplace' in kwargs:
+        del kwargs['inplace']
+    return _original_set_axis(self, labels, *args, **kwargs)
+pd.DataFrame.set_axis = _set_axis_patched
+
+import abagen.images
+
+def _labeltable_to_df_patched(labels):
+    """
+    Patched version of abagen.utils.labeltable_to_df to handle missing 0 index
+    and use pd.concat instead of append.
+    """
+    info = pd.DataFrame(columns=['id', 'label', 'hemisphere', 'structure'])
+    for table, hemi in zip(labels, ('L', 'R')):
+        if len(table) == 0:
+            continue
+        ids, label = zip(*table.items())
+        new_df = pd.DataFrame(dict(id=ids, label=label, hemisphere=hemi, structure='cortex'))
+        info = pd.concat([info, new_df], ignore_index=True)
+        
+    # Use errors='ignore' to handle missing 0
+    info = info.set_index('id').drop([0], axis=0, errors='ignore').sort_index()
+
+    if len(info) != 0:
+        return info
+
+abagen.images.labeltable_to_df = _labeltable_to_df_patched
+
+
+import collections
 from abagen import check_atlas, get_expression_data
 from brainspace.mesh.mesh_io import read_surface, write_surface
 from sklearn.model_selection import ParameterGrid
+from nibabel.gifti import GiftiImage, GiftiDataArray
 
 from brainstat._utils import data_directories, logger
 from brainstat.datasets.base import (
@@ -23,7 +69,7 @@ def surface_genetic_expression(
     surfaces: Optional[Union[str, Sequence[str]]] = None,
     space: Optional[str] = None,
     *,
-    atlas_info: str = None,
+    atlas_info: Optional[str] = None,
     ibf_threshold: float = 0.5,
     probe_selection: str = "diff_stability",
     donor_probes: str = "aggregate",
@@ -89,52 +135,90 @@ def surface_genetic_expression(
     elif surfaces is None:
         surfaces = []
 
-    surfaces_gii = []
-    for surface in surfaces:
-        if not isinstance(surface, str) and not isinstance(surface, Path):
-            # Rather roundabout deletion of the temporary file for Windows compatibility.
+    temp_files = []
+    try:
+        if isinstance(labels, np.ndarray):
+            # Assuming 'labels' is a 1D NumPy array of length 20484
+            num_vertices = len(labels)  # Should be 20484
+            half_size = num_vertices // 2  # Half of 20484, which is 10242
+
+            # Split the array into two halves
+            labels_left = labels[:half_size]  # First half for the left hemisphere
+            labels_right = labels[half_size:]  # Second half for the right hemisphere
+
+            # Create GiftiDataArrays for each hemisphere
+            data_array_left = GiftiDataArray(data=labels_left)
+            data_array_right = GiftiDataArray(data=labels_right)
+
+            # Create separate GiftiImages for each hemisphere
+            labels_left_gii = GiftiImage(darrays=[data_array_left])
+            labels_right_gii = GiftiImage(darrays=[data_array_right])
+            
+            # Save to temporary files for abagen compatibility
+            labels_files = []
+            for img in [labels_left_gii, labels_right_gii]:
+                f = tempfile.NamedTemporaryFile(suffix=".gii", delete=False)
+                f.close()
+                nib.save(img, f.name)
+                labels_files.append(f.name)
+                temp_files.append(f.name)
+            labels = tuple(labels_files)
+    
+        surfaces_gii = []
+        for surface in surfaces:
+            if not isinstance(surface, str) and not isinstance(surface, Path):
+                # Cast surface data to float32 to comply with GIFTI standard
+                # GIFTI only supports uint8, int32, and float32 datatypes
+                if hasattr(surface, 'Points') and surface.Points.dtype != np.float32:
+                    surface = surface.copy()
+                    surface.Points = surface.Points.astype(np.float32)
+                
+                f = tempfile.NamedTemporaryFile(suffix=".gii", delete=False)
+                f.close()
+                write_surface(surface, f.name, otype="gii")
+                surfaces_gii.append(f.name)
+                temp_files.append(f.name)
+            else:
+                surfaces_gii.append(surface)
+
+        # Use abagen to grab expression data.
+        logger.info(
+            "If you use BrainStat's genetics functionality, please cite abagen (https://abagen.readthedocs.io/en/stable/citing.html)."
+        )
+        atlas = check_atlas(labels, geometry=surfaces_gii, space=space)
+        expression = get_expression_data(
+            atlas,
+            atlas_info=atlas_info,
+            ibf_threshold=ibf_threshold,
+            probe_selection=probe_selection,
+            donor_probes=donor_probes,
+            lr_mirror=lr_mirror,
+            missing=missing,
+            tolerance=tolerance,
+            sample_norm=sample_norm,
+            gene_norm=gene_norm,
+            norm_matched=norm_matched,
+            norm_structures=norm_structures,
+            region_agg=region_agg,
+            agg_metric=agg_metric,
+            corrected_mni=corrected_mni,
+            reannotated=reannotated,
+            return_counts=return_counts,
+            return_donors=return_donors,
+            return_report=return_report,
+            donors=donors,
+            data_dir=data_dir,
+            verbose=verbose,
+            n_proc=n_proc,
+        )
+
+        return expression
+    finally:
+        for f in temp_files:
             try:
-                with tempfile.NamedTemporaryFile(suffix=".gii", delete=False) as f:
-                    name = f.name
-                    write_surface(surface, name, otype="gii")
-                surfaces_gii.append(nib.load(name))
-            finally:
-                Path(name).unlink()
-        else:
-            surfaces_gii.append(nib.load(surface))
-
-    # Use abagen to grab expression data.
-    logger.info(
-        "If you use BrainStat's genetics functionality, please cite abagen (https://abagen.readthedocs.io/en/stable/citing.html)."
-    )
-    atlas = check_atlas(labels, geometry=surfaces_gii, space=space)
-    expression = get_expression_data(
-        atlas,
-        atlas_info=atlas_info,
-        ibf_threshold=ibf_threshold,
-        probe_selection=probe_selection,
-        donor_probes=donor_probes,
-        lr_mirror=lr_mirror,
-        missing=missing,
-        tolerance=tolerance,
-        sample_norm=sample_norm,
-        gene_norm=gene_norm,
-        norm_matched=norm_matched,
-        norm_structures=norm_structures,
-        region_agg=region_agg,
-        agg_metric=agg_metric,
-        corrected_mni=corrected_mni,
-        reannotated=reannotated,
-        return_counts=return_counts,
-        return_donors=return_donors,
-        return_report=return_report,
-        donors=donors,
-        data_dir=data_dir,
-        verbose=verbose,
-        n_proc=n_proc,
-    )
-
-    return expression
+                Path(f).unlink()
+            except FileNotFoundError:
+                pass
 
 
 def __create_precomputed(

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/context/histology.py

@@ -156,7 +156,19 @@ def read_histology_profile(
         )
 
     with h5py.File(histology_file, "r") as h5_file:
-        profiles = h5_file.get(template)[...]
+        if template == "fslr32k":
+            # Known issue #369: The fslr32k data file on the server actually contains
+            # fs_LR_64k resolution data (64984 vertices) instead of fs_LR_32k (32492 vertices).
+            # This is a data hosting issue. Users expecting 32k resolution data should be aware
+            # that they will receive 64k resolution data until this is fixed on the server.
+            logger.warning(
+                "Known issue: The fslr32k histology profile data currently contains "
+                "fs_LR_64k resolution (64984 vertices) instead of fs_LR_32k (32492 vertices). "
+                "See https://github.com/MICA-MNI/BrainStat/issues/369 for details."
+            )
+            profiles = h5_file.get("fs_LR_64k")[...]
+        else:
+            profiles = h5_file.get(template)[...]
         if civet_template:
             fsaverage_surface = fetch_template_surface("fsaverage")
             civet_surface = fetch_template_surface(civet_template)
@@ -191,7 +203,16 @@ def download_histology_profiles(
 
     data_dir = Path(data_dir) if data_dir else data_directories["BIGBRAIN_DATA_DIR"]
     data_dir.mkdir(parents=True, exist_ok=True)
-    output_file = data_dir / ("histology_" + template + ".h5")
+    if template == "fslr32k":
+        output_file = data_dir / "histology_fslr32k.h5"
+        # Known issue #369: warn users about data resolution mismatch
+        logger.warning(
+            "Note: The fslr32k histology profile data currently contains "
+            "fs_LR_64k resolution (64984 vertices) instead of fs_LR_32k. "
+            "See https://github.com/MICA-MNI/BrainStat/issues/369 for details."
+        )
+    else:
+        output_file = data_dir / ("histology_" + template + ".h5")
 
     url = read_data_fetcher_json()["bigbrain_profiles"][template]["url"]
 

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/datasets/base.py

@@ -1,6 +1,8 @@
 """ Load external datasets. """
+import json
 import tempfile
 import zipfile
+from collections import namedtuple
 from pathlib import Path
 from typing import List, Optional, Tuple, Union
 
@@ -11,9 +13,19 @@ from brainspace.mesh.mesh_io import read_surface
 from brainspace.mesh.mesh_operations import combine_surfaces
 from brainspace.vtk_interface.wrappers.data_object import BSPolyData
 from netneurotools import datasets as nnt_datasets
-from netneurotools.civet import read_civet
 from nibabel import load as nib_load
 from nibabel.freesurfer.io import read_annot, read_geometry
+from sklearn.utils import Bunch
+
+try:
+    from netneurotools.datasets.utils import _get_data_dir, _get_dataset_info
+except ImportError:
+    from netneurotools.datasets.datasets_utils import _get_data_dir, _get_dataset_info
+
+try:
+    from nilearn.datasets._utils import fetch_files as _fetch_files
+except ImportError:
+    from nilearn.datasets.utils import fetch_files as _fetch_files
 
 from brainstat._utils import (
     _download_file,
@@ -24,6 +36,65 @@ from brainstat._utils import (
 from brainstat.mesh.interpolate import _surf2surf
 
 
+def read_civet(fname: Union[str, Path]) -> Tuple[np.ndarray, np.ndarray]:
+    """
+    Reads a CIVET surface file (MNI OBJ format).
+
+    Parameters
+    ----------
+    fname : str or Path
+        Path to the CIVET surface file.
+
+    Returns
+    -------
+    vertices : numpy.ndarray
+        (N, 3) array of vertex coordinates.
+    faces : numpy.ndarray
+        (M, 3) array of face indices.
+    """
+    fname = str(fname)
+    with open(fname, "rb") as f:
+        first_char = f.read(1)
+
+    if first_char == b"P":
+        with open(fname, "r") as f:
+            content = f.read().split()
+
+        n_vertices = int(content[6])
+
+        idx = 7
+        # Vertices
+        vertices = np.array(content[idx : idx + n_vertices * 3], dtype=float).reshape(
+            -1, 3
+        )
+        idx += n_vertices * 3
+
+        # Normals
+        idx += n_vertices * 3
+
+        n_triangles = int(content[idx])
+        idx += 1
+
+        color_flag = int(content[idx])
+        idx += 1
+
+        if color_flag == 0:
+            idx += 4
+        else:
+            idx += n_vertices * 4
+
+        # Check remaining items to decide if we need to skip
+        remaining = len(content) - idx
+        if remaining == n_triangles * 3 + n_triangles:
+            idx += n_triangles
+
+        triangles = np.array(content[idx:], dtype=int).reshape(-1, 3)
+
+        return vertices, triangles
+    else:
+        raise NotImplementedError("Binary CIVET files are not supported yet.")
+
+
 def fetch_parcellation(
     template: str,
     atlas: str,
@@ -147,7 +218,7 @@ def fetch_template_surface(
         surfaces_fs = [read_geometry(file) for file in surface_files]
         surfaces = [build_polydata(surface[0], surface[1]) for surface in surfaces_fs]
     elif template == "fslr32k":
-        surfaces = [read_surface(file) for file in surface_files]
+        surfaces = [read_surface(str(file)) for file in surface_files]
     else:
         surfaces_obj = [read_civet(file) for file in surface_files]
         surfaces = [build_polydata(surface[0], surface[1]) for surface in surfaces_obj]
@@ -384,7 +455,7 @@ def _fetch_template_surface_files(
 
     if template == "fslr32k":
         layer = layer if layer else "midthickness"
-        bunch = nnt_datasets.fetch_conte69(data_dir=str(data_dir))
+        bunch = _fetch_conte69_fixed(data_dir=str(data_dir))
     elif template == "civet41k" or template == "civet164k":
         layer = layer if layer else "mid"
         if layer == "sphere":
@@ -515,3 +586,43 @@ def _fetch_civet_spheres(template: str, data_dir: Path) -> Tuple[str, str]:
 
     # Return two filenames to conform to other left/right hemisphere functions.
     return (str(filename), str(filename))
+
+
+SURFACE = namedtuple('Surface', ('lh', 'rh'))
+
+
+def _fetch_conte69_fixed(data_dir=None, url=None, resume=True, verbose=1):
+    """
+    Download files for Van Essen et al., 2012 Conte69 template.
+    Fixed version to handle encoding on Windows.
+    """
+    dataset_name = 'tpl-conte69'
+    keys = ['midthickness', 'inflated', 'vinflated']
+
+    data_dir = _get_data_dir(data_dir=data_dir)
+    info = _get_dataset_info(dataset_name)
+    if url is None:
+        url = info['url']
+
+    opts = {
+        'uncompress': True,
+        'md5sum': info['md5'],
+        'move': '{}.tar.gz'.format(dataset_name)
+    }
+
+    filenames = [
+        'tpl-conte69/tpl-conte69_space-MNI305_variant-fsLR32k_{}.{}.surf.gii'
+        .format(res, hemi) for res in keys for hemi in ['L', 'R']
+    ] + ['tpl-conte69/template_description.json']
+
+    data = _fetch_files(data_dir, files=[(f, url, opts) for f in filenames],
+                        resume=resume, verbose=verbose)
+
+    # Fix: Specify encoding='utf-8'
+    with open(data[-1], 'r', encoding='utf-8') as src:
+        data[-1] = json.load(src)
+
+    # bundle hemispheres together
+    data = [SURFACE(*data[:-1][i:i + 2]) for i in range(0, 6, 2)] + [data[-1]]
+
+    return Bunch(**dict(zip(keys + ['info'], data)))

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/mesh/interpolate.py

@@ -13,7 +13,7 @@ from brainspace.mesh.mesh_elements import get_cells, get_points
 from brainspace.mesh.mesh_io import read_surface
 from brainspace.vtk_interface.wrappers.data_object import BSPolyData
 from nilearn.datasets import load_mni152_brain_mask
-from scipy.interpolate.ndgriddata import LinearNDInterpolator, NearestNDInterpolator
+from scipy.interpolate import LinearNDInterpolator, NearestNDInterpolator
 from scipy.spatial import cKDTree
 
 from brainstat._typing import ArrayLike

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/stats/_linear_model.py

@@ -442,7 +442,9 @@ def _compute_resls(self, Y: np.ndarray) -> Tuple[np.ndarray, dict]:
     for j in range(Y.shape[2]):
         normr = np.sqrt(self.SSE[((j + 1) * (j + 2) // 2) - 1])
         for i in range(Y.shape[0]):
-            u = Y[i, :, j] / normr
+            u = np.divide(
+                Y[i, :, j], normr, out=np.zeros_like(Y[i, :, j]), where=normr != 0
+            )
             resl[:, j] += np.diff(u[edges], axis=1).ravel() ** 2
 
     return resl, mesh_connections

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/stats/_multiple_comparisons.py

@@ -951,7 +951,7 @@ def peak_clus(
         cluster_val = cluster_val + 1
 
     vox = np.argwhere(excurset) + 1
-    ivox = np.argwhere(np.in1d(vox, lmvox)) + 1
+    ivox = np.argwhere(np.isin(vox.flatten(), lmvox)) + 1
     clmid = nf[ivox - 1]
     uclmid, iclmid, jclmid = np.unique(clmid, return_index=True, return_inverse=True)
     iclmid = iclmid + 1
@@ -959,7 +959,7 @@ def peak_clus(
     ucid = np.unique(nf)
     nclus = len(ucid)
     # implementing matlab's histc function ###
-    bin_edges = np.r_[-np.Inf, 0.5 * (ucid[:-1] + ucid[1:]), np.Inf]
+    bin_edges = np.r_[-np.inf, 0.5 * (ucid[:-1] + ucid[1:]), np.inf]
     ucvol, ucvol_edges = np.histogram(nf, bin_edges)
 
     if reselspvert is None:

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/stats/_t_test.py

@@ -173,6 +173,6 @@ def _t_test(self) -> None:
                 M[M_ef] = ef_duplicate[:, i]
                 M[M_sse] = sse_matrix.flatten()
 
-                self.t[i] = np.sqrt(-np.linalg.det(M) / det_sse / vf)
+                self.t[i] = float(np.sqrt(-np.linalg.det(M) / det_sse / vf))
 
     self.t = np.atleast_2d(self.t)

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/stats/terms.py

@@ -240,7 +240,7 @@ def remove_duplicate_columns(df: pd.DataFrame, tol: float = 1e-8) -> List[str]:
     df = df / df.abs().sum(0)
     df *= 1 / tol
     # keep = df.round().T.drop_duplicates(keep="last").T.columns  # Slow!!
-    idx = np.unique(df.round().values, axis=1, return_index=True)[-1]
+    idx = np.unique(df.round().to_numpy(dtype=float), axis=1, return_index=True)[-1]
     keep = df.columns[sorted(idx)]
     return keep
 
@@ -365,9 +365,14 @@ class FixedEffect(object):
         return self._add(t)
 
     def __radd__(
-        self, t: Union[ArrayLike, "FixedEffect", "MixedEffect"]
+        self, t: Union[int, ArrayLike, "FixedEffect", "MixedEffect"]
     ) -> "FixedEffect":
-        return self._add(t, side="right")
+        if isinstance(t, int) and t == 0:
+            # When t is 0, return self without adding an extra intercept
+            return self
+        else:
+            # For other cases, proceed with the addition
+            return self._add(t, side="right")
 
     def __sub__(self, t: Union[ArrayLike, "FixedEffect"]) -> "FixedEffect":
         if self.empty:
@@ -377,12 +382,16 @@ class FixedEffect(object):
             return self
         df /= df.abs().sum(0)
         df.index = self.m.index
-
         m = self.m / self.m.abs().sum(0)
-        merged = m.T.merge(df.T, how="outer", indicator=True)
-        mask = (merged._merge.values == "left_only")[: self.m.shape[1]]
+
+        m_normalized_T = m.T
+        df_normalized_T = df.T
+
+        merged = m_normalized_T.merge(df_normalized_T, how="outer", indicator=True)
+        merged_index = m_normalized_T.iloc[:, [1]].reset_index().merge(merged, how="left")
+        mask = merged_index.loc[merged_index['_merge'] == 'left_only','index']
         return FixedEffect(
-            self.m[self.m.columns[mask]], add_intercept=False, _check_categorical=False
+            self.m[mask], add_intercept=False, _check_categorical=False
         )
 
     def _mul(

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/stats/utils.py

@@ -101,7 +101,7 @@ def ismember(
 
     else:
         # Get values of A that are in B.
-        bool_vector = np.in1d(A, B)
+        bool_vector = np.isin(A, B)
         bool_array = np.reshape(bool_vector, A.shape)
 
         # Get location of elements in B. Transpose B and A to get MATLAB behavior (i.e. column first)
@@ -110,7 +110,9 @@ def ismember(
         locations = np.zeros(A.size) + np.nan
         Aflat = A.T.flat
         for i in range(0, idx.size):
-            locations[idx[i]] = locB[np.argwhere(val == Aflat[idx[i]])]
+            matches = np.argwhere(val == Aflat[idx[i]])
+            if len(matches) > 0:
+                locations[idx[i]] = locB[matches[0, 0]]
         locations = np.reshape(locations, A.shape)
     return bool_array, locations
 

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/tests/test_SLM.py

@@ -7,10 +7,12 @@ import numpy as np
 import pandas as pd
 import pytest
 import templateflow.api as tflow
+from sklearn.linear_model import LinearRegression
 
 from brainstat.stats.SLM import SLM, _onetailed_to_twotailed
 from brainstat.stats.terms import FixedEffect, MixedEffect
 from brainstat.tests.testutil import datadir
+from brainstat.tutorial.utils import fetch_mics_data
 
 
 def recursive_comparison(X1, X2):
@@ -123,6 +125,31 @@ def dummy_test(infile, expfile):
     assert all(flag == True for (flag) in testout)
 
 
+def dummy_test2():
+
+    # BrainStat
+    thickness, demographics = fetch_mics_data()
+    term_age = FixedEffect(demographics.AGE_AT_SCAN)
+    model = term_age
+    slm_age = SLM(
+        model,
+        np.ones(thickness.shape[0]),
+        surf="fsaverage5",
+    )
+    slm_age.fit(thickness)
+
+    # Scikit Learn
+    model_age = LinearRegression()
+    model_age.fit(demographics.AGE_AT_SCAN.to_numpy().reshape(-1, 1), thickness)
+
+    # Compare
+    comp2 = np.allclose(
+        np.squeeze(model_age.coef_), slm_age.coef[1, :], rtol=1e-05, equal_nan=True
+    )
+
+    assert comp2 == True
+
+
 expected_number_of_tests = 22
 parametrize = pytest.mark.parametrize
 
@@ -134,6 +161,10 @@ def test_run_all(test_number):
     dummy_test(infile, expfile)
 
 
+# Test against scikit learn
+dummy_test2()
+
+
 @pytest.mark.skipif(
     sys.platform.startswith("win"), reason="Template flow has issues on windows."
 )

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/tests/test_datasets.py

@@ -19,6 +19,7 @@ parametrize = pytest.mark.parametrize
 def test_load_surfaces(template):
     """Test loading surface templates. For now this only tests whether it runs
     without error and whether the output type is correct."""
+    
     surface = fetch_template_surface(template, join=True)
     assert isinstance(surface, BSPolyData)
 

brainstat-0.5.2/brainstat/tests/test_genetics.py

@@ -0,0 +1,33 @@
+from brainstat.context.genetics import surface_genetic_expression
+from brainstat.datasets import fetch_parcellation, fetch_template_surface, fetch_parcellation
+import numpy as np
+from nilearn import datasets
+import pytest
+from urllib.error import HTTPError
+
+# Get Schaefer-100 genetic expression.
+# def test_surface_genetic_expression():
+#     schaefer_100_fs5 = fetch_parcellation("fsaverage5", "schaefer", 100)
+#     surfaces = fetch_template_surface("fsaverage5", join=False)
+#     expression = surface_genetic_expression(schaefer_100_fs5, surfaces, space="fsaverage")
+#     assert expression is not None
+
+
+def test_surface_genetic_expression2():
+    destrieux = datasets.fetch_atlas_surf_destrieux()
+    labels = np.hstack((destrieux['map_left'], destrieux['map_right']))
+    fsaverage = datasets.fetch_surf_fsaverage()
+    surfaces = (fsaverage['pial_left'], fsaverage['pial_right'])
+    
+    try:
+        expression = surface_genetic_expression(labels, surfaces, space='fsaverage')
+        assert expression is not None
+    except HTTPError as e:
+        if e.code == 503:
+            pytest.skip(f"Allen Brain Institute server unavailable (503): {e}")
+        else:
+            raise
+
+if __name__ == "__main__":
+    test_surface_genetic_expression2()
+    # test_surface_genetic_expression()

brainstat-0.5.2/brainstat/tests/test_histology.py

@@ -0,0 +1,32 @@
+"""Unit tests for the histology module."""
+import pytest
+import requests
+import numpy as np
+
+from brainstat._utils import read_data_fetcher_json
+from brainstat.context.histology import read_histology_profile
+parametrize = pytest.mark.parametrize
+json = read_data_fetcher_json()
+
+
+@parametrize("template", list(json["bigbrain_profiles"].keys()))
+def test_urls(template):
+    """Tests whether the histology files can be downloaded.
+
+    Parameters
+    ----------
+    template : list
+        Template names.
+    """
+    try:
+        r = requests.get(json["bigbrain_profiles"][template]["url"], timeout=10, stream=True)
+        assert r.status_code == 200
+    except (requests.exceptions.ConnectionError, requests.exceptions.Timeout):
+        pytest.skip(f"Network connection issue when testing URL for {template}")
+
+
+def test_histology_profiles_is_ndarray():
+    histology_profiles = read_histology_profile(template="fslr32k")
+    
+    # Assert that histology_profiles is an ndarray
+    assert isinstance(histology_profiles, np.ndarray), "histology_profiles should be a NumPy ndarray"

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/tests/test_mesh_edges.py

@@ -81,4 +81,4 @@ def test_nifti_input():
     edg = mesh_edges(nifti)
 
     assert edg.shape[1] == 2
-    assert np.amax(edg) <= nifti.get_data().sum() - 1
+    assert np.amax(edg) <= nifti.get_fdata().sum() - 1

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/tests/test_terms.py

@@ -2,7 +2,8 @@
 
 import numpy as np
 import pandas as pd
-
+from functools import reduce
+from brainstat.tutorial.utils import fetch_mics_data
 from brainstat.stats.terms import FixedEffect, MixedEffect
 
 
@@ -29,8 +30,10 @@ def test_fixed_init():
 
 def test_fixed_overload():
     """Tests the overloads of the FixedEffect class."""
+    np.random.seed(2)
     random_data = np.random.random_sample((10, 3))
     fix01 = FixedEffect(random_data[:, :2], ["x0", "x1"], add_intercept=False)
+    fix012 = FixedEffect(random_data, ["x0", "x1", "x2"], add_intercept=False)
     fix12 = FixedEffect(random_data[:, 1:], ["x2", "x3"], add_intercept=False)
     fix2 = FixedEffect(random_data[:, 2], ["x2"], add_intercept=False)
     fixi0 = FixedEffect(random_data[:, 0], ["x0"], add_intercept=True)
@@ -47,7 +50,20 @@ def test_fixed_overload():
     assert np.array_equal(fix_add_intercept.m, expected)
 
     fix_sub = fix01 - fix12
-    assert np.array_equal(fix_sub.m, random_data[:, 0][:, None])
+    np.testing.assert_allclose(
+        fix_sub.m,
+        random_data[:, 0][:, None],
+        atol=1e-8,
+        rtol=1e-5,
+    )
+
+    fix_sub2 = fix012 - fix2
+    np.testing.assert_allclose(
+        fix_sub2.m,
+        random_data[:, :2],
+        atol=1e-8,
+        rtol=1e-5,
+    )
 
     fix_mul = fix01 * fix2
     assert np.array_equal(fix_mul.m, random_data[:, :2] * random_data[:, 2][:, None])
@@ -129,3 +145,11 @@ def test_identity_detection():
 def as_variance(M):
     var = [np.reshape(x[:, None] @ x[None, :], (-1, 1)) for x in M.T]
     return np.squeeze(var, axis=2).T
+
+
+def test_sum():
+    _, demographics = fetch_mics_data()
+    model = []
+    term_age = FixedEffect(demographics.AGE_AT_SCAN)
+    model.append(term_age)
+    assert reduce(lambda x, y: x + y, model) == sum(model)

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat/tutorial/utils.py

@@ -56,7 +56,7 @@ def fetch_mics_data(
 
 def fetch_abide_data(
     data_dir: Optional[Union[str, Path]] = None,
-    sites: Sequence[str] = None,
+    sites: Optional[Sequence[str]] = None,
     keep_control: bool = True,
     keep_patient: bool = True,
     overwrite: bool = False,

{brainstat-0.4.2 → brainstat-0.5.2/brainstat.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: brainstat
-Version: 0.4.2
+Version: 0.5.2
 Summary: A toolbox for statistical analysis of neuroimaging data
 Home-page: https://github.com/MICA-LAB/BrainStat
 Author: MNI-MICA Lab and MPI-CNG Lab
@@ -13,13 +13,44 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: Topic :: Scientific/Engineering
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Requires-Python: >=3.7.*
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: abagen>=0.1
+Requires-Dist: brainspace>=0.1.2
+Requires-Dist: h5py
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: netneurotools<0.3.0
+Requires-Dist: neurosynth
+Requires-Dist: nibabel
+Requires-Dist: nilearn>=0.7.0
+Requires-Dist: nimare
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: scikit_learn>=1.0
+Requires-Dist: scipy>=1.7
+Requires-Dist: templateflow
+Requires-Dist: trimesh
+Provides-Extra: dev
+Requires-Dist: gitpython; extra == "dev"
+Requires-Dist: hcp-utils; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: plotly; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 BrainStat : A toolbox for statistical analysis of neuroimaging data
 ===================================================================

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat.egg-info/SOURCES.txt

@@ -53,6 +53,7 @@ brainstat/tests/test_SLM.py
 brainstat/tests/test_datasets.py
 brainstat/tests/test_f_test.py
 brainstat/tests/test_fdr.py
+brainstat/tests/test_genetics.py
 brainstat/tests/test_histology.py
 brainstat/tests/test_linear_model.py
 brainstat/tests/test_mesh_edges.py

{brainstat-0.4.2 → brainstat-0.5.2}/brainstat.egg-info/requires.txt

@@ -1,15 +1,16 @@
 abagen>=0.1
 brainspace>=0.1.2
 h5py
-netneurotools
+matplotlib>=3.4
+netneurotools<0.3.0
 neurosynth
 nibabel
 nilearn>=0.7.0
 nimare
-numpy>=1.16.5
-pandas
-scikit_learn
-scipy>=1.3.3
+numpy>=1.21
+pandas>=1.3
+scikit_learn>=1.0
+scipy>=1.7
 templateflow
 trimesh
 

{brainstat-0.4.2 → brainstat-0.5.2}/setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-description-file = README.rst
+description_file = README.rst
 license_files = LICENSE
 
 [mypy]

{brainstat-0.4.2 → brainstat-0.5.2}/setup.py

@@ -31,24 +31,23 @@ setuptools.setup(
         "Intended Audience :: Developers",
         "Topic :: Software Development :: Build Tools",
         "Topic :: Scientific/Engineering",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
-    python_requires=">=3.7.*",
+    python_requires=">=3.10",
     install_requires=[
         "abagen>=0.1",
         "brainspace>=0.1.2",
         "h5py",
-        "netneurotools",
+        "matplotlib>=3.4",
+        "netneurotools<0.3.0",
         "neurosynth",
         "nibabel",
         "nilearn>=0.7.0",
         "nimare",
-        "numpy>=1.16.5",
-        "pandas",
-        "scikit_learn",
-        "scipy>=1.3.3",
+        "numpy>=1.21",
+        "pandas>=1.3",
+        "scikit_learn>=1.0",
+        "scipy>=1.7",
         "templateflow",
         "trimesh",
     ],

brainstat-0.4.2/brainstat/tests/test_histology.py

@@ -1,21 +0,0 @@
-"""Unit tests for the histology module."""
-import pytest
-import requests
-
-from brainstat._utils import read_data_fetcher_json
-
-parametrize = pytest.mark.parametrize
-json = read_data_fetcher_json()
-
-
-@parametrize("template", list(json["bigbrain_profiles"].keys()))
-def test_urls(template):
-    """Tests whether the histology files can be downloaded.
-
-    Parameters
-    ----------
-    template : list
-        Template names.
-    """
-    r = requests.head(json["bigbrain_profiles"][template]["url"])
-    assert r.status_code == 200