junifer 0.0.6.dev11__py3-none-any.whl → 0.0.6.dev19__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.dev11'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev11')
+__version__ = version = '0.0.6.dev19'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev19')

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-0.0.6.dev11.dist-info → junifer-0.0.6.dev19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev11
+Version: 0.0.6.dev19
 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.dev11.dist-info → junifer-0.0.6.dev19.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=-T9XmiCCL0j3YLx-0Pph15sPfL5FlcBDscajjJ-V4sU,604
-junifer/_version.py,sha256=mU31Rbo9393TgDvfpsOHnq8SiUzPPQ4wTt9IrlhivXo,426
+junifer/_version.py,sha256=wZWyCHAcc7iLZxm5FymgJmboZgMFn19f87418KPqxDg,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
@@ -267,10 +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.dev11.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev11.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev11.dist-info/METADATA,sha256=JERhQXlkyOo07_IQ5HaJksc0Eg9v9IWV45ZyodsOxmU,8279
-junifer-0.0.6.dev11.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-junifer-0.0.6.dev11.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.6.dev11.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev11.dist-info/RECORD,,
+junifer-0.0.6.dev19.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev19.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev19.dist-info/METADATA,sha256=Fqi240THeyTkrkoQLR87j1ybgjdR-_m5DMeWgy1JTHc,8279
+junifer-0.0.6.dev19.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+junifer-0.0.6.dev19.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.6.dev19.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev19.dist-info/RECORD,,