junifer 0.0.6.dev6__py3-none-any.whl → 0.0.6.dev16__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev6'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev6')
+__version__ = version = '0.0.6.dev16'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev16')

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -13,7 +13,7 @@ from nilearn.connectome import (
     prec_to_partial,
     sym_matrix_to_vec,
 )
-from scipy import linalg
+from scipy import linalg, stats
 from sklearn.base import clone
 from sklearn.covariance import EmpiricalCovariance
 
@@ -314,15 +314,18 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
     * default ``cov_estimator`` is
       :class:`sklearn.covariance.EmpiricalCovariance`
     * default ``kind`` is ``"correlation"``
+    * supports Spearman's correlation via ``kind="spearman correlation"``
 
     Parameters
     ----------
     cov_estimator : estimator object, optional
         The covariance estimator
         (default ``EmpiricalCovariance(store_precision=False)``).
-    kind : {"covariance", "correlation", "partial correlation", \
-            "tangent", "precision"}, optional
-        The matrix kind. For the use of ``"tangent"`` see [1]_
+    kind : {"covariance", "correlation", "spearman correlation", \
+            "partial correlation", "tangent", "precision"}, optional
+        The matrix kind. The default value uses Pearson's correlation.
+        If ``"spearman correlation"`` is used, the data will be ranked before
+        estimating the covariance. For the use of ``"tangent"`` see [1]_
         (default "correlation").
     vectorize : bool, optional
         If True, connectivity matrices are reshaped into 1D arrays and only
@@ -400,17 +403,22 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
             self.cov_estimator_ = clone(self.cov_estimator)
 
         # Compute all the matrices, stored in "connectivities"
-        if self.kind == "correlation":
-            covariances_std = [
-                self.cov_estimator_.fit(
-                    signal.standardize_signal(
-                        x,
-                        detrend=False,
-                        standardize=self.standardize,
-                    )
-                ).covariance_
-                for x in X
-            ]
+        if self.kind in ["correlation", "spearman correlation"]:
+            covariances_std = []
+            for x in X:
+                x = signal.standardize_signal(
+                    x,
+                    detrend=False,
+                    standardize=self.standardize,
+                )
+
+                # rank data if spearman correlation
+                # before calculating covariance
+                if self.kind == "spearman correlation":
+                    x = stats.rankdata(x, axis=0)
+
+                covariances_std.append(self.cov_estimator_.fit(x).covariance_)
+
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
         else:
             covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -71,6 +71,7 @@ CONNECTIVITY_KINDS = (
     "tangent",
     "precision",
     "partial correlation",
+    "spearman correlation",
 )
 
 N_FEATURES = 49

junifer/onthefly/__init__.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 from .read_transform import read_transform
+from . import _brainprint as brainprint
 
 
-__all__ = ["read_transform"]
+__all__ = ["read_transform", "brainprint"]

junifer/onthefly/_brainprint.py

@@ -0,0 +1,141 @@
+"""Provide onthefly functions for BrainPrint post-analysis."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import TYPE_CHECKING, Dict, Optional, Type
+
+import numpy as np
+import pandas as pd
+
+from ..utils import raise_error
+
+
+if TYPE_CHECKING:
+    from junifer.storage import BaseFeatureStorage
+
+
+__all__ = ["normalize", "reweight"]
+
+
+def normalize(
+    storage: Type["BaseFeatureStorage"],
+    features: Dict[str, Dict[str, Optional[str]]],
+    kind: str,
+) -> pd.DataFrame:
+    """Read stored brainprint data and normalize either surfaces or volumes.
+
+    Parameters
+    ----------
+    storage : storage-like
+        The storage class, for example, :class:`.HDF5FeatureStorage`.
+    features : dict, optional
+        The feature names or MD5 hashes to read as dict.
+        The dict should have the keys:
+
+        * ``"areas"`` (if ``kind="surface"``)
+        * ``"volumes"`` (if ``kind="volume"``)
+        * ``"eigenvalues"``
+
+        and the corresponding value for each of the keys is again
+        a dict with the keys:
+
+        * ``"feature_name"`` : str or None
+        * ``"feature_md5"`` : str or None
+
+        Either one of ``"feature_name"`` or ``"feature_md5"`` needs to be
+        not None for each first-level key, but both keys are mandatory.
+
+    kind : {"surface", "volume"}
+        The kind of normalization.
+
+    Returns
+    -------
+    pandas.DataFrame
+        The transformed feature as a ``pandas.DataFrame``.
+
+    Raises
+    ------
+    ValueError
+        If ``kind`` is invalid.
+
+    """
+    # Read storage
+    data_dict = {}
+    for k, v in features.items():
+        data_dict[k] = storage.read_df(**v)  # type: ignore
+
+    # Check and normalize
+    valid_kind = ["surface", "volume"]
+    normalized_df = None
+    if kind == "surface":
+        eigenvalues_df = data_dict["eigenvalues"]
+        areas_df = data_dict["areas"]
+        normalized_df = eigenvalues_df.combine(
+            areas_df, lambda left, right: left * right
+        )
+    elif kind == "volume":
+        eigenvalues_df = data_dict["eigenvalues"]
+        volumes_df = data_dict["volumes"]
+        normalized_df = eigenvalues_df.combine(
+            volumes_df, lambda left, right: left * right ** np.divide(2.0, 3.0)
+        )
+    else:
+        raise_error(
+            "Invalid value for `kind`, should be one of: " f"{valid_kind}"
+        )
+
+    return normalized_df
+
+
+def reweight(
+    storage: Type["BaseFeatureStorage"],
+    feature_name: Optional[str] = None,
+    feature_md5: Optional[str] = None,
+) -> pd.DataFrame:
+    """Read stored brainprint data and reweight eigenvalues.
+
+    Parameters
+    ----------
+    storage : storage-like
+        The storage class, for example, :class:`.HDF5FeatureStorage`.
+    feature_name : str, optional
+        Name of the feature to read (default None).
+    feature_md5 : str, optional
+        MD5 hash of the feature to read (default None).
+
+    Returns
+    -------
+    pandas.DataFrame
+        The transformed feature as a ``pandas.DataFrame``.
+
+    """
+    # Read storage
+    eigenvalues_df = storage.read_df(
+        feature_name=feature_name, feature_md5=feature_md5
+    )  # type: ignore
+
+    # Create data for operation
+    exploded_count_idx_df = (
+        eigenvalues_df.reset_index("eigenvalue")
+        .index.value_counts()
+        .apply(lambda x: np.arange(1, x + 1).astype(float))
+        .to_frame()
+        .explode("count")
+    )
+    idx_data = (
+        pd.concat(
+            [exploded_count_idx_df] * len(eigenvalues_df.columns), axis=1
+        )
+        .reset_index()
+        .drop("subject", axis=1, inplace=False)
+        .to_numpy()
+    )
+    idx_df = pd.DataFrame(
+        data=idx_data,
+        index=eigenvalues_df.index,
+        columns=eigenvalues_df.columns,
+    )
+
+    # Combine
+    return eigenvalues_df.combine(idx_df, lambda left, right: left / right)

{junifer-0.0.6.dev6.dist-info → junifer-0.0.6.dev16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev6
+Version: 0.0.6.dev16
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev6.dist-info → junifer-0.0.6.dev16.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=-T9XmiCCL0j3YLx-0Pph15sPfL5FlcBDscajjJ-V4sU,604
-junifer/_version.py,sha256=nVn_509eHiH2KjeZJLZwflBXCcWgR8aVl2f9Ym1ItyM,424
+junifer/_version.py,sha256=6F6uOGNcjX6dbq-EmRB3esRKologELcdzkhY7J6HmO0,426
 junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
 junifer/api/__init__.py,sha256=lwyIF0hPc7fICuSoddJfay0LPqlTRxHJ_xbtizgFYZA,312
 junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
@@ -134,9 +134,9 @@ junifer/external/h5io/h5io/_version.py,sha256=mFY0GwwuN-a3M8w93_mskS6GZIvv9SNdjL
 junifer/external/h5io/h5io/chunked_array.py,sha256=K1HWf7R2Jc7gCzBqAoBjx0ZnMmUhTe3iAO6RF6PdUO4,3338
 junifer/external/h5io/h5io/chunked_list.py,sha256=1Y5BbuWzurJlEFQzJNuDdC3fNZ39ENEMba99X_4VeSM,1952
 junifer/external/nilearn/__init__.py,sha256=UdUKYArx3hvcziln89iaSGZcNGwHvsmbB4E5gS1zvOs,321
-junifer/external/nilearn/junifer_connectivity_measure.py,sha256=y6MSWz_7YjRNfahLiS8_ptmEBoSBqhj6J9E0p7cN1Jw,16847
+junifer/external/nilearn/junifer_connectivity_measure.py,sha256=c8aLIlSs2eo6uHj-ZtYAto4szjbj21Zlj5JTQRrAnu8,17322
 junifer/external/nilearn/junifer_nifti_spheres_masker.py,sha256=DbSK2hKrgpHZ_vCRLbVv3YJpLZNkEAG0HFfQQpG6zdU,16546
-junifer/external/nilearn/tests/test_junifer_connectivity_measure.py,sha256=cwm-RMSHLS6GF-z2ioSNln3N9WoSrLf41mGvyYYMd7w,33918
+junifer/external/nilearn/tests/test_junifer_connectivity_measure.py,sha256=yBsi9g_31UDo_oG7K6eKRp36CZ28G5cbNcKM3aTT53s,33946
 junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py,sha256=zpvBYIvaNjUj9fIUg5K78LRzJqbyMYlUo2UQYS9_lo4,12275
 junifer/markers/__init__.py,sha256=u4BFgS_3GXAwFN2HfqdAhlBkyenLw4IYlMlwXwnjkVQ,1235
 junifer/markers/base.py,sha256=__Z0owDdjTwb7alQneOeoaUqaeCVbHwFRnaRZERi37M,8364
@@ -206,7 +206,8 @@ junifer/markers/tests/test_marker_utils.py,sha256=SR3ADWI3uGv4ozYqVu-rMZnJVqP6Jn
 junifer/markers/tests/test_markers_base.py,sha256=XYe1Z_88h2g1WX6Em4aM8VMyBuCpy5sNHbbpC0I89m4,2979
 junifer/markers/tests/test_parcel_aggregation.py,sha256=FkB0O0HjTk1CnLOn-dzNs_9_byUOISRc4jV92shN2Kc,27655
 junifer/markers/tests/test_sphere_aggregation.py,sha256=TGn5S7zKK0SJ4nHIxRZQSCpqRBmz7c8Sb8C79dLoHjE,10611
-junifer/onthefly/__init__.py,sha256=WykjD_q_zWyX40Y5iKsFXhPJLzD1NPcN-XKFKZDMXfc,184
+junifer/onthefly/__init__.py,sha256=TA6tPuw54ynDlumb9Ii-2p59hw2rGoCMe1-vQ89JzZ8,238
+junifer/onthefly/_brainprint.py,sha256=-q5j5xOkuZD_f-pjWi-b8VRqM9ZXDk1TnccuQDfLwz4,3860
 junifer/onthefly/read_transform.py,sha256=kZ-N_fKe9glaBTjhj_HXrdTtWXGI-fMoBpsawcOgsTw,4340
 junifer/onthefly/tests/test_read_transform.py,sha256=D2C3IpXQHdsJSF07v8rEwGntLGXjZOserlRhebJUAVM,4719
 junifer/pipeline/__init__.py,sha256=mmhtYuRGetBmBvKPVb9MxklcEK_R9ly-dgkzQiOp3g8,363
@@ -266,10 +267,10 @@ junifer/utils/logging.py,sha256=ardaiJkDfZMYvak5UIL5Etxg5Ii7inmVQSBdFLdgtb8,9781
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev6.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev6.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev6.dist-info/METADATA,sha256=xiXPBGQgwXibZ7Lv-Jh8gMDr17N_ExAeOOHaDUG-KPE,8278
-junifer-0.0.6.dev6.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-junifer-0.0.6.dev6.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.6.dev6.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev6.dist-info/RECORD,,
+junifer-0.0.6.dev16.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev16.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev16.dist-info/METADATA,sha256=aKu6mGcLd9lgmR5bN_3DPrnsQTbWteKq9f_tdfHXYV0,8279
+junifer-0.0.6.dev16.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+junifer-0.0.6.dev16.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.6.dev16.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev16.dist-info/RECORD,,