brainstat 0.3.6__tar.gz → 0.5.2__tar.gz

{brainstat-0.3.6/brainstat.egg-info → brainstat-0.5.2}/PKG-INFO

@@ -1,26 +1,56 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: brainstat
-Version: 0.3.6
+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
-Author-email: reinder.vosdewael@gmail.com, sheymaba@gmail.com
+Author-email: saratheriver@gmail.com, sheymaba@gmail.com
 License: BSD 3-Clause License
 Project-URL: Documentation, https://brainstat.readthedocs.io
 Project-URL: Bug Reports, https://github.com/MICA-LAB/BrainStat/issues
 Project-URL: Source, https://github.com/MICA-LAB/BrainStat/
-Platform: UNKNOWN
 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
 ===================================================================
@@ -60,11 +90,12 @@ Developers
 ----------
 .. |seyma_s|   unicode:: U+015E .. CEDILLA S
 
-- Reinder Vos de Wael - MICA Lab, Montreal Neurological Institute
+- Sara Lariviere - MICA Lab, Montreal Neurological Institute
 - |seyma_s|\ eyma Bayrak - Max Planck Institute for Human Cognitive and Brain Sciences 
+- Reinder Vos de Wael - MICA Lab, Montreal Neurological Institute
 - Oualid Benkarim - MICA Lab, Montreal Neurological Institute
-- Sara Lariviere - MICA Lab, Montreal Neurological Institute
 - Raul Cruces - MICA Lab, Montreal Neurological Institute
+- Jessica Royer - MICA Lab, Montreal Neurological Institute
 - Peer Herholz - Montreal Neurological Institute 
 - Seok-Jun Hong - Sungkyunkwan University
 - Sofie Valk - Max Planck Institute for Human Cognitive and Brain Sciences
@@ -84,5 +115,3 @@ Support
 If you have problems installing the software or questions about usage and
 documentation, or something else related to BrainStat, you can post to the
 `Issues <https://github.com/MICA-MNI/BrainStat/issues>`_ section of our repository.
-
-

{brainstat-0.3.6 → brainstat-0.5.2}/README.rst

@@ -36,11 +36,12 @@ Developers
 ----------
 .. |seyma_s|   unicode:: U+015E .. CEDILLA S
 
-- Reinder Vos de Wael - MICA Lab, Montreal Neurological Institute
+- Sara Lariviere - MICA Lab, Montreal Neurological Institute
 - |seyma_s|\ eyma Bayrak - Max Planck Institute for Human Cognitive and Brain Sciences 
+- Reinder Vos de Wael - MICA Lab, Montreal Neurological Institute
 - Oualid Benkarim - MICA Lab, Montreal Neurological Institute
-- Sara Lariviere - MICA Lab, Montreal Neurological Institute
 - Raul Cruces - MICA Lab, Montreal Neurological Institute
+- Jessica Royer - MICA Lab, Montreal Neurological Institute
 - Peer Herholz - Montreal Neurological Institute 
 - Seok-Jun Hong - Sungkyunkwan University
 - Sofie Valk - Max Planck Institute for Human Cognitive and Brain Sciences

{brainstat-0.3.6 → brainstat-0.5.2}/brainstat/__init__.py

@@ -1,2 +1,2 @@
 """Neuroimaging statistics toolbox."""
-__version__ = "0.3.6"
+__version__ = "0.5.2"

{brainstat-0.3.6 → brainstat-0.5.2}/brainstat/_utils.py

@@ -56,8 +56,8 @@ def generate_data_fetcher_json() -> None:
             "glasser": {
                 "fsaverage": {
                     "url": (
-                        "https://box.bic.mni.mcgill.ca/s/y2NMHXr47WOCtpp/download",
-                        "https://box.bic.mni.mcgill.ca/s/Y0Fmd2tIF69Mqpt/download",
+                        "https://box.bic.mni.mcgill.ca/s/j4nfMA4D7jSx3QZ/download",
+                        "https://box.bic.mni.mcgill.ca/s/qZTplkH4A4exOnF/download",
                     ),
                 },
                 "fsaverage5": {
@@ -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-0.5.2/brainstat/context/genetics.py

@@ -0,0 +1,301 @@
+"""Genetic decoding using abagen."""
+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 (
+    _fetch_template_surface_files,
+    _valid_parcellations,
+    fetch_parcellation,
+)
+
+
+def surface_genetic_expression(
+    labels: Union[Sequence[str], np.ndarray],
+    surfaces: Optional[Union[str, Sequence[str]]] = None,
+    space: Optional[str] = None,
+    *,
+    atlas_info: Optional[str] = None,
+    ibf_threshold: float = 0.5,
+    probe_selection: str = "diff_stability",
+    donor_probes: str = "aggregate",
+    lr_mirror: Optional[bool] = None,
+    missing: Optional[str] = None,
+    tolerance: float = 2,
+    sample_norm: str = "srs",
+    gene_norm: str = "srs",
+    norm_matched: bool = True,
+    norm_structures: bool = False,
+    region_agg: str = "donors",
+    agg_metric: str = "mean",
+    corrected_mni: bool = True,
+    reannotated: bool = True,
+    return_counts: bool = False,
+    return_donors: bool = False,
+    return_report: bool = False,
+    donors: str = "all",
+    data_dir: Optional[str] = None,
+    verbose: float = 0,
+    n_proc: int = 1
+) -> pd.DataFrame:
+    """Computes genetic expression of surface parcels.
+
+    Parameters
+    ----------
+    labels : list-of-str or numpy.ndarray
+        List of paths to label files for the parcellation, or numpy array
+        containing the pre-loaded labels
+    surfaces : list-of-image, optional
+        List of paths to surface files or preloaded surfaces. If not specified
+        assumes that `labels` are on the `fsaverage5` surface. Default: None
+    space : {'fsaverage', 'fslr'}
+        What template space `surfaces` are aligned to. If not specified assumes
+        that `labels` are on the `fsaverage5` surface. Default: None
+
+    For details of the remaining parameters please consult the
+    abagen.get_expression_data() documentation. All its parameters bar "atlas"
+    are valid input parameters.
+
+    Returns
+    -------
+    pandas.DataFrame
+        Dataframe containing the expression of each gene within each region.
+
+    Examples
+    --------
+    >>> from brainstat.context.genetics import surface_genetic_expression
+    >>> from nilearn import datasets
+    >>> import numpy as np
+
+    >>> 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'])
+    >>> expression = surface_genetic_expression(labels, surfaces,
+    ...                                         space='fsaverage')
+    """
+
+    # Deal with the input parameters.
+    if isinstance(surfaces, str):
+        surfaces = [surfaces]
+    elif surfaces is None:
+        surfaces = []
+
+    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:
+                Path(f).unlink()
+            except FileNotFoundError:
+                pass
+
+
+def __create_precomputed(
+    data_dir: Optional[Union[str, Path]] = None,
+    output_dir: Optional[Union[str, Path]] = None,
+) -> None:
+    """Creates precomputed matrices of genetic expression for standard atlases. These are
+    used for the MATLAB implementation."""
+
+    if output_dir is None:
+        output_dir = data_dir = (
+            Path(data_dir) if data_dir else data_directories["BRAINSTAT_DATA_DIR"]
+        )
+
+    # Get all parcellations in a format compatible with ParameterGrid.
+    parcellations = _valid_parcellations()
+    for key in parcellations:
+        parcellations[key].update({"atlas": [key]})
+        if key == "schaefer":
+            parcellations[key].update({"seven_networks": (True, False)})
+        else:
+            parcellations[key].update({"seven_networks": (True,)})
+
+        # We only really need to compute this for one template surface.
+        # We'll use fsaverage5 for all.
+        parcellations[key].update({"surfaces": ["fsaverage5"]})
+
+    param_grid = ParameterGrid(list(parcellations.values()))
+
+    # Compute expression for all parcellations.
+    for params in param_grid:
+        if params["atlas"] == "schaefer":
+            network_tag = "7Networks" if params["seven_networks"] else "17Networks"
+        else:
+            network_tag = ""
+
+        filename_components = filter(
+            None,
+            (
+                "expression",
+                params["atlas"],
+                str(params["n_regions"]),
+                network_tag,
+            ),
+        )
+
+        filename = "_".join(filename_components) + ".csv.gz"
+        output_file = Path(output_dir) / filename
+        if output_file.exists():
+            print('Skipping "{}"'.format(output_file))
+            continue
+        else:
+            print('Computing "{}"'.format(output_file))
+
+        surface_files = _fetch_template_surface_files(
+            params["surfaces"], data_dir=data_dir  # type: ignore
+        )
+        space = "fslr" if params["surfaces"] == "fslr32k" else "fsaverage"
+
+        labels = fetch_parcellation(
+            params["surfaces"],
+            params["atlas"],
+            params["n_regions"],
+            seven_networks=params["seven_networks"],
+            data_dir=data_dir,
+        )
+
+        surf_lh = tempfile.NamedTemporaryFile(suffix=".surf.gii")
+        surf_rh = tempfile.NamedTemporaryFile(suffix=".surf.gii")
+        for i, surf in enumerate((surf_lh, surf_rh)):
+            __freesurfer_to_surfgii(surface_files[i], surf.name)
+        surface_paths = [surf_lh.name, surf_rh.name]
+
+        expression = surface_genetic_expression(labels, surface_paths, space=space)  # type: ignore
+        expression.to_csv(output_file)  # type: ignore
+
+
+def __freesurfer_to_surfgii(freesurfer_file: str, gifti_file: str) -> None:
+    surf = read_surface(freesurfer_file, itype="fs")
+    write_surface(surf, gifti_file, otype="gii")

{brainstat-0.3.6 → 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-0.3.6 → brainstat-0.5.2}/brainstat/context/meta_analysis.py

@@ -11,7 +11,9 @@ import numpy as np
 import pandas as pd
 import templateflow.api as tflow
 from brainspace.vtk_interface.wrappers.data_object import BSPolyData
-from scipy.stats.stats import pearsonr
+from scipy.stats.stats import pearsonr, spearmanr
+from math import pi
+import matplotlib.pyplot as plt
 
 from brainstat._utils import (
     data_directories,
@@ -25,6 +27,7 @@ from brainstat.mesh.interpolate import _surf2vol, multi_surface_to_volume
 def meta_analytic_decoder(
     template: str,
     stat_labels: np.ndarray,
+    corrtype: Optional[str] = "pearson",
     data_dir: Optional[Union[str, Path]] = None,
 ):
     """Meta-analytic decoding of surface maps using NeuroSynth or NeuroQuery.
@@ -36,6 +39,8 @@ def meta_analytic_decoder(
     stat_labels : str, numpy.ndarray, sequence of str or numpy.ndarray
         Path to a label file for the surfaces, numpy array containing the
         labels, or a list containing multiple of the aforementioned.
+    corrtype : str, optional
+        Correlation type {'pearson', 'spearman'}. Default is 'pearson'.
     data_dir : str, optional
         The directory of the dataset. If none exists, a new dataset will
         be downloaded and saved to this path. If None, the directory defaults to
@@ -74,9 +79,14 @@ def meta_analytic_decoder(
             | np.isnan(stat_vector)
             | np.isinf(stat_vector)
         )
-        correlations[i], _ = pearsonr(stat_vector[keep], feature_data[keep])
-
-    df = pd.DataFrame(correlations, index=feature_names, columns=["Pearson's r"])
+        if corrtype == "pearson":
+            correlations[i], _ = pearsonr(stat_vector[keep], feature_data[keep])
+            colname = "Pearson's r"
+        elif corrtype == "spearman":
+            correlations[i], _ = spearmanr(stat_vector[keep], feature_data[keep])
+            colname = "Spearman's r"
+
+    df = pd.DataFrame(correlations, index=feature_names, columns=[colname])
     return df.sort_values(by="Pearson's r", ascending=False)
 
 
@@ -224,3 +234,86 @@ def _fetch_precomputed_neurosynth(data_dir: Path) -> Generator[Path, None, None]
             (Path(name)).unlink()
 
     return data_dir.glob("Neurosynth_TFIDF__*z_desc-consistency.nii.gz")
+
+
+def radar_plot(data=None, title="", axis_range=None, label=None, color=(0, 0, 0)):
+    """Visualize data in radar plot (author: @saratheriver)
+    Parameters
+    ----------
+    data : ndarray, shape = (n_val,)
+        Data.
+    title : string, optional
+        Title of spider plot. Default is empty.
+    axis_range : tuple, optional
+        Range of spider plot axes. Default is (min, max).
+    label : list, optional
+        List of axis labels. Length = same as data.shape[0]. Default is empty.
+    color : tuple, optional
+        Color of line. Default is (0, 0, 0).
+
+    Returns
+    -------
+    class_mean : ndarray, shape = (data.shape[0],)
+        Values for each branch.
+    figure
+        Spider plot.
+    """
+    # Data check
+    if data is None:
+        print("Need data to plot")
+
+    # Create dataframe
+    class_mean = pd.DataFrame(data=data.T, columns=label)
+
+    # Number of variable
+    categories = list(class_mean)
+    N = len(categories)
+
+    # We are going to plot the first line of the data frame.
+    # But we need to repeat the first value to close the circular graph:
+    values = class_mean.loc[0].values.flatten().tolist()
+    values += values[:1]
+
+    # What will be the angle of each axis in the plot? (we divide the plot / number of variable)
+    angles = [n / float(N) * 2 * pi for n in range(N)]
+    angles += angles[:1]
+
+    # Initialise the spider plot
+    plt.figure(figsize=(8, 4))
+    ax = plt.subplot(111, polar=True)
+    ax.spines["polar"].set_visible(False)
+
+    # Draw one axe per variable + add labels labels yet
+    if label is None:
+        label = list(class_mean)
+
+    plt.xticks(angles[:-1], label, color="black", size=12)
+    ax.xaxis.get_majorticklabels()[0].set_horizontalalignment("left")
+    ax.xaxis.get_majorticklabels()[2].set_verticalalignment("bottom")
+    ax.xaxis.get_majorticklabels()[3].set_verticalalignment("top")
+
+    # Draw ylabels
+    ax.set_rlabel_position(0)
+    if axis_range is None:
+        axis_range = (np.min(values), np.max(values))
+
+    inc = (axis_range[1] - axis_range[0]) / 4
+    newinc = [
+        axis_range[0] + inc,
+        axis_range[0] + (inc * 2),
+        axis_range[0] + (inc * 3),
+        axis_range[0],
+    ]
+    plt.yticks(
+        newinc, [str("{:.2f}".format(elem)) for elem in newinc], color="grey", size=10
+    )
+    plt.ylim(axis_range)
+
+    # add title
+    if title:
+        plt.title(title)
+
+    # Plot data
+    ax.plot(angles, values, linewidth=3, linestyle="solid", color=color)
+
+    return class_mean

{brainstat-0.3.6 → brainstat-0.5.2}/brainstat/data/data_urls.json

@@ -53,8 +53,8 @@
         "glasser": {
             "fsaverage": {
                 "url": [
-                    "https://box.bic.mni.mcgill.ca/s/y2NMHXr47WOCtpp/download",
-                    "https://box.bic.mni.mcgill.ca/s/Y0Fmd2tIF69Mqpt/download"
+                    "https://box.bic.mni.mcgill.ca/s/j4nfMA4D7jSx3QZ/download",
+                    "https://box.bic.mni.mcgill.ca/s/qZTplkH4A4exOnF/download"
                 ]
             },
             "fsaverage5": {