Merge pull request #89 from effigies/fix/double_mode_partial_fix

FIX: Center phase maps around central mode, avoiding FoV-related outliers

Author: effigies

.circleci/config.yml

@@ -374,33 +374,36 @@ jobs:
             fi
 
   test_package:
-    machine:
-      image: circleci/classic:201711-01
+    docker:
+      - image: circleci/python:3.7.4
     working_directory: /tmp/src/sdcflows
     steps:
       - checkout
       - run:
           name: Setup Python environment with virtualenvs
           command: |
-            pyenv global 3.5.2
-            python3 -m pip install --upgrade virtualenv
+            python -m pip install --user --upgrade virtualenv pip
       - run:
           name: Prepare build environment
           command: |
             virtualenv --python=python3 /tmp/build
             source /tmp/build/bin/activate
             python3 -m pip install "setuptools>=30.3.0" "pip>=10.0.1" twine docutils
       - run:
-          name: Prepare install environment
+          name: Prepare install environments
           command: |
-            virtualenv --python=python3 /tmp/install
-            source /tmp/install/bin/activate
+            virtualenv --python=python3 /tmp/install_sdist
+            source /tmp/install_sdist/bin/activate
+            python3 -m pip install "setuptools>=30.3.0" "pip>=10.0.1"
+            deactivate
+            virtualenv --python=python3 /tmp/install_wheel
+            source /tmp/install_wheel/bin/activate
             python3 -m pip install "setuptools>=30.3.0" "pip>=10.0.1"
       - run:
           name: Build SDCflows in build environment
           command: |
             source /tmp/build/bin/activate
-            python setup.py sdist
+            python setup.py sdist bdist_wheel
       - store_artifacts:
           path: /tmp/src/sdcflows/dist
       - run:
@@ -411,11 +414,25 @@ jobs:
       - run:
           name: Install sdist package into install environment and check version
           command: |
-            source /tmp/install/bin/activate
+            source /tmp/install_sdist/bin/activate
             THISVERSION=$( python get_version.py )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             pip install dist/sdcflows*.tar.gz
-            which sdcflows | grep install\\/bin
+            which sdcflows | grep install_sdist\\/bin
+            INSTALLED_VERSION=$(sdcflows --version)
+            INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
+            INSTALLED_VERSION=${INSTALLED_VERSION#*"sdcflows v"}
+            echo "VERSION: \"$THISVERSION\""
+            echo "INSTALLED: \"$INSTALLED_VERSION\""
+            test "$INSTALLED_VERSION" = "v$THISVERSION"
+      - run:
+          name: Install wheel into install environment and check version
+          command: |
+            source /tmp/install_wheel/bin/activate
+            THISVERSION=$( python get_version.py )
+            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
+            pip install dist/sdcflows*.whl
+            which sdcflows | grep install_wheel\\/bin
             INSTALLED_VERSION=$(sdcflows --version)
             INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
             INSTALLED_VERSION=${INSTALLED_VERSION#*"sdcflows v"}

sdcflows/interfaces/fmap.py

@@ -661,19 +661,31 @@ def _delta_te(in_values, te1=None, te2=None):
 
 def au2rads(in_file, newpath=None):
     """Convert the input phase difference map in arbitrary units (a.u.) to rads."""
-    from scipy.stats import mode
+    from scipy import stats
     im = nb.load(in_file)
     data = im.get_fdata(dtype='float32')
     hdr = im.header.copy()
 
-    # First center data around 0.0.
-    data -= mode(data, axis=None)[0][0]
+    dmin, dmax = data.min(), data.max()
+
+    # Find the mode ignoring outliers on the far max/min, to allow for junk outside the FoV
+    fudge = 0.05 * (dmax - dmin)
+    mode = stats.mode(data[(data > dmin + fudge) & (data < dmax - fudge)])[0][0]
+
+    # Center data around 0.0
+    data -= mode
+
+    # Provide a less opaque error if we still can't figure it out
+    neg = data < 0
+    pos = data > 0
+    if not (neg.any() and pos.any()):
+        raise ValueError("Could not find an appropriate mode to center phase values around")
 
     # Scale lower tail
-    data[data < 0] = - np.pi * data[data < 0] / data[data < 0].min()
+    data[neg] = - np.pi * data[neg] / data[neg].min()
 
     # Scale upper tail
-    data[data > 0] = np.pi * data[data > 0] / data[data > 0].max()
+    data[pos] = np.pi * data[pos] / data[pos].max()
 
     # Offset to 0 - 2pi
     data += np.pi