Merge branch 'master' into v1.4

.ci/test_template.sh

@@ -2,17 +2,6 @@
 
 set -e
 
-# Install $PY_VERSION, xvfb, and all
-# of the wxpython dependencies.
-apt-get update -y || true
-apt-get install -y software-properties-common python-software-properties xvfb libgtk2.0-0 libnotify4 freeglut3 libsdl1.2debian
-add-apt-repository -y ppa:deadsnakes/ppa
-apt-get update -y || true
-apt-get install -y $PY_VERSION "$PY_VERSION"-dev $PY_PACKAGES
-$PY_VENV test.venv
-source test.venv/bin/activate
-pip install --upgrade pip setuptools
-
 # If running on a fork repository, we merge in the
 # upstream/master branch. This is done so that merge
 # requests from fork to the parent repository will
@@ -23,7 +12,7 @@ if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
   git merge --no-commit --no-ff upstream/master;
 fi;
 
-$INSTALL_WX
+source /test.venv/bin/activate
 
 # All other deps can be installed as normal.
 # We install test dependenciesd through pip,

.gitlab-ci.yml

@@ -16,6 +16,11 @@
 #    5. deploy: Uploading the build outputs to pypi/hosting servers, and the
 #               documentation to a hosting server.
 #
+# Custom docker images are used for several jobs - these images are
+# available at:
+#
+#    https://hub.docker.com/u/pauldmccarthy/
+#
 # The test and style stages are executed on all branches of upstream and fork
 # repositories.
 #
@@ -81,12 +86,6 @@ stages:
 #   - TWINE_PASSWORD:                - Password to use when uploading to pypi
 #
 #   - TWINE_REPOSITORY_URL:          - Pypi repository to upload to
-#
-#   - WXPYTHON_UBUNTU1404_URL:       - Url to a location containg binary wheels
-#                                      for wxPython/ubuntu 14.04
-#
-#   - WXPYTHON_UBUNTU1604_URL:       - Url to a location containg binary wheels
-#                                      for wxPython/ubuntu 16.04
 ###############################################################################
 
 
@@ -161,48 +160,26 @@ variables:
 
 test:2.7:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py27-wxpy4-gtk2
   <<: *test_template
-  variables:
-    PY_VERSION:  "python2.7"
-    PY_PACKAGES: "python-pip python-virtualenv"
-    PY_VENV:     "virtualenv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
 
 
-# we use ubuntu:14.04 for python 3.4, because
-# wxpython is not available for 16.04/3.4
 test:3.4:
   stage: test
-  image: ubuntu:14.04
+  image: pauldmccarthy/fsleyes-py34-wxpy4-gtk2
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.4"
-    PY_PACKAGES: "python3-pip python3.4-venv"
-    PY_VENV:     "python3.4 -m venv"
-    INSTALL_WX:  "pip install --pre -f $WXPYTHON_UBUNTU1404_URL wxpython"
 
 
 test:3.5:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.5"
-    PY_PACKAGES: "python3-pip python3-venv"
-    PY_VENV:     "python3.5 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
 
 
 test:3.6:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk2
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.6"
-    PY_PACKAGES: "python3-pip python3.6-venv"
-    PY_VENV:     "python3.6 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
 
 
 #############
@@ -212,13 +189,9 @@ test:3.6:
 
 style:
   stage: style
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
   <<: *test_template
   variables:
-    PY_VERSION:  "python3.5"
-    PY_PACKAGES: "python3-pip python3-venv"
-    PY_VENV:     "python3.5 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
     TEST_STYLE:  "true"
 
 

CHANGELOG.rst

@@ -2,19 +2,28 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
-1.4.1 (Thursday 9th November 2017)
+1.4.2 (Monday December 4th 2017)
+--------------------------------
+
+
+* New function :func:`.transform.rmsdev` function, which implements the RMS
+  deviation equation for comparing two affine transformations (FMRIB Technical
+  Report TR99MJ1, available at https://www.fmrib.ox.ac.uk/datasets/techrep/).
+
+
+1.4.1 (Thursday November 9th 2017)
 ----------------------------------
 
 
 * Fixed bug in ``setup.py``.
 
 
-1.4.0 (Thursday 9th November 2017)
+1.4.0 (Thursday November 9th 2017)
 ----------------------------------
 
 
-* The :func:`.uniquePrefix` function now raises a :exc:`.PathError` instead
-  of a :exc:`.ValueError`, when an invalid path is provided.
+* The :func:`.uniquePrefix` function now raises a :exc:`~.path.PathError`
+  instead of a :exc:`.ValueError`, when an invalid path is provided.
 * The :mod:`fsl.utils.async` module is now deprecated, as ``async`` will
   become a reserved word in Python 3.7. It has been renamed to
   ``fsl.utils.idle``, with no other API changes.
@@ -32,7 +41,7 @@ order.
   if incompatible shapes are provided.
 
 
-1.3.1 (Wednesday 25th October 2017)
+1.3.1 (Wednesday October 25th 2017)
 -----------------------------------
 
 
@@ -40,7 +49,7 @@ order.
   ``WX_UNKNOWN``.
 
 
-1.3.0 (Wednesday 25th October 2017)
+1.3.0 (Wednesday October 25th 2017)
 -----------------------------------
 
 

fsl/utils/settings.py

@@ -372,7 +372,7 @@ class Settings(object):
         try:
             with open(configFile, 'rb') as f:
                 return pickle.load(f)
-        except (IOError, pickle.UnpicklingError):
+        except (IOError, pickle.UnpicklingError, EOFError):
             log.debug('Unable to load stored {} configuration file '
                       '{}'.format(self.__configID, configFile),
                       exc_info=True)
@@ -391,7 +391,7 @@ class Settings(object):
         try:
             with open(configFile, 'wb') as f:
                 pickle.dump(config, f)
-        except (IOError, pickle.PicklingError):
+        except (IOError, pickle.PicklingError, EOFError):
             log.warning('Unable to save {} configuration file '
                         '{}'.format(self.__configID, configFile),
                         exc_info=True)

fsl/utils/transform.py

@@ -23,6 +23,7 @@ spaces. The following functions are provided:
    axisBounds
    flirtMatrixToSform
    sformToFlirtMatrix
+   rmsdev
 
 And a few more functions are provided for working with vectors:
 
@@ -593,3 +594,49 @@ def sformToFlirtMatrix(srcImage, refImage, srcXform=None):
                   refWorldToVoxMat,
                   srcVoxToWorldMat,
                   srcScaledVoxToVoxMat)
+
+
+def rmsdev(T1, T2, R=None, xc=None):
+    """Calculates the RMS deviation of the given affine transforms ``T1`` and
+    ``T2``. This can be used as a measure of the 'distance' between two
+    affines.
+
+    The ``T1`` and ``T2`` arguments may be either full ``(4, 4)`` affines, or
+    ``(3, 3)`` rotation matrices.
+
+    See FMRIB technical report TR99MJ1, available at:
+
+    https://www.fmrib.ox.ac.uk/datasets/techrep/
+
+    :arg T1:  First affine
+    :arg T2:  Second affine
+    :arg R:   Sphere radius
+    :arg xc:  Sphere centre
+    :returns: The RMS deviation between ``T1`` and ``T2``.
+    """
+
+    if R is None:
+        R = 1
+
+    if xc is None:
+        xc = np.zeros(3)
+
+    # rotations only
+    if T1.shape == (3, 3):
+        M = np.dot(T2, invert(T1)) - np.eye(3)
+        A = M[:3, :3]
+        t = np.zeros(3)
+
+    # full affine
+    else:
+        M = np.dot(T2, invert(T1)) - np.eye(4)
+        A = M[:3, :3]
+        t = M[:3,  3]
+
+    Axc = np.dot(A, xc)
+
+    erms = np.dot((t + Axc).T, t + Axc)
+    erms = 0.2 * R ** 2 * np.dot(A.T, A).trace() + erms
+    erms = np.sqrt(erms)
+
+    return erms

fsl/version.py

@@ -41,7 +41,7 @@ import            re
 import            string
 
 
-__version__ = '1.4.1'
+__version__ = '1.4.2'
 """Current version number, as a string. """
 
 

tests/test_transform.py

@@ -537,3 +537,34 @@ def test_sformToFlirtMatrix():
 
         assert np.all(np.isclose(result1, expected))
         assert np.all(np.isclose(result2, expected))
+
+
+def test_rmsdev():
+
+    t1 = np.eye(4)
+    t2 = transform.scaleOffsetXform([1, 1, 1], [2, 0, 0])
+
+    assert np.isclose(transform.rmsdev(t1, t2), 2)
+    assert np.isclose(transform.rmsdev(t1, t2, R=2), 2)
+    assert np.isclose(transform.rmsdev(t1, t2, R=2, xc=(1, 1, 1)), 2)
+
+    t1       = np.eye(3)
+    lastdist = 0
+
+    for i in range(1, 11):
+        rot    = np.pi * i / 10.0
+        t2     = transform.axisAnglesToRotMat(rot, 0, 0)
+        result = transform.rmsdev(t1, t2)
+
+        assert result > lastdist
+
+        lastdist = result
+
+    for i in range(11, 20):
+        rot    = np.pi * i / 10.0
+        t2     = transform.axisAnglesToRotMat(rot, 0, 0)
+        result = transform.rmsdev(t1, t2)
+
+        assert result < lastdist
+
+        lastdist = result