pyAFQ 1.1__tar.gz → 1.2__tar.gz

{pyAFQ-1.1 → pyAFQ-1.2}/.github/workflows/docbuild.yml

@@ -20,7 +20,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[all]
         conda install -c conda-forge xvfbwrapper
     - name: Build docs
       env:

{pyAFQ-1.1 → pyAFQ-1.2}/.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser]
+        pip install .[all]
     - name: Nibabel pre-release installation
       if: ${{ matrix.nibabel-pre }}
       run: |

{pyAFQ-1.1 → pyAFQ-1.2}/AFQ/_fixes.py

@@ -292,13 +292,13 @@ def gaussian_weights(bundle, n_points=100, return_mahalnobis=False,
         # This should come back as a 3D covariance matrix with the spatial
         # variance covariance of this node across the different streamlines,
         # reorganized as an upper diagonal matrix for expected Mahalanobis
-        v_inv = np.triu(np.cov(sls[:, i, :].T, ddof=0))
+        cov = np.cov(sls[:, i, :].T, ddof=0)
 
         # calculate Mahalanobis for node in every fiber
-        if np.linalg.matrix_rank(v_inv) == n_dim:
-            v_inv = np.linalg.inv(v_inv)
+        if np.any(cov > 0):
+            ci = np.linalg.inv(cov)
 
-            dist = (diff[:, i, :] @ v_inv) * diff[:, i, :]
+            dist = (diff[:, i, :] @ ci) * diff[:, i, :]
             weights[:, i] = np.sqrt(np.sum(dist, axis=1))
 
         # In the special case where all the streamlines have the exact same

pyAFQ-1.2/AFQ/afq_bids_entities.json

@@ -0,0 +1,22 @@
+{
+    "name": "bidsafq",
+    "entities": [
+      {
+        "name": "odfmodel",
+        "pattern": "[_/\\\\]+odfmodel-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "coordsys",
+        "pattern": "[_/\\\\]+coordsys-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "trkmethod",
+        "pattern": "[_/\\\\]+trkmethod-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "recogmethod",
+        "pattern": "[_/\\\\]+recogmethod-([a-zA-Z0-9]+)"
+      }
+    ]
+  }
+