Merge pull request #221 from larsoner/imsave

MRG: Fix imsave

.travis.yml

@@ -1,27 +1,38 @@
 language: c
 sudo: false
-# This list of requirements is way overkill, but it helps ensure we
-# actually load a usable config (it works for MNE-Python)
+
 env:
     global: PYTHON_VERSION=2.7
             DISPLAY=:99.0
-            CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov nose coverage"
-            PIP_DEPENDENCIES="codecov nibabel imageio"
 
 matrix:
     include:
+        # Full (Linux, 3.6)
+        - os: linux
+          env: CONDA_ENVIRONMENT="environment.yml"
+          addons:
+            apt:
+              packages:
+                - mencoder
+
         # Full (Linux, 2.7)
         - os: linux
+          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov nose coverage"
+               PIP_DEPENDENCIES="codecov nibabel imageio"
           addons:
             apt:
               packages:
                 - mencoder
 
         # Minimal (no mencoder)
         - os: linux
+          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov nose coverage"
+               PIP_DEPENDENCIES="codecov nibabel"
 
         # OSX
         - os: osx
+          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov nose coverage"
+               PIP_DEPENDENCIES="codecov nibabel imageio"
 
 # Setup anaconda
 before_install:
@@ -46,7 +57,9 @@ before_script:
     - unzip ../fsaverage_min.zip
     - cd ..
     - export SUBJECTS_DIR="${PWD}/subjects"
-    - python -c "import imageio; imageio.plugins.ffmpeg.download()"
+    - if [[ $PIP_DEPENDENCIES == *"imageio"* ]] || [ ! -z "$CONDA_ENVIRONMENT" ]; then
+        python -c "import imageio; imageio.plugins.ffmpeg.download()";
+      fi
 
 script:
     - cd ${SRC_DIR}

appveyor.yml

@@ -18,6 +18,7 @@ install:
   - "conda install ffmpeg -c conda-forge"
   - "SET SUBJECTS_DIR=%CD%\\subjects"
   - "ls %CD%\\subjects"
+  - "pip install --upgrade git+https://github.com/enthought/mayavi.git"
 
 build: false  # Not a C# project, build stuff at the test step instead.
 

doc/install.rst

@@ -40,7 +40,6 @@ To use PySurfer, you will need to have the following Python packages:
 
 * numpy_
 * scipy_
-* ipython_
 * nibabel_
 * mayavi_
 * matplotlib_

environment.yml

@@ -0,0 +1,29 @@
+name: mne
+channels:
+- defaults
+- clinicalgraphics  # Needed for VTK
+dependencies:
+- python=3.6.1
+- pip
+- mkl
+- numpy
+- scipy
+- matplotlib
+- pyqt=5
+- vtk>=7
+- nose
+- coverage
+- pytest
+- pytest-cov
+- flake8
+- pygments
+- pip:
+  - "git+https://github.com/enthought/traits.git@a7a83182048c08923953e302658b51b68c802132"
+  - "git+https://github.com/enthought/pyface.git@13a064de48adda3c880350545717d8cf8929afad"
+  - "git+https://github.com/enthought/traitsui.git@ee8ef0a34dfc1db18a8e2c0301cc18d96b7a3e2f"
+  - "git+https://github.com/enthought/mayavi.git"
+  - nibabel
+  - pytest-sugar
+  - pytest-faulthandler
+  - imageio
+  - codecov

surfer/tests/test_viz.py

@@ -38,19 +38,26 @@ def has_freesurfer():
 
 def _set_backend(backend=None):
     """Use testing backend for Windows."""
+    only_test = (sys.platform == 'win32' or
+                 (os.getenv('TRAVIS', 'false') == 'true' and
+                  sys.version[0] == '3'))
     if backend is None:
-        backend = 'test' if sys.platform == 'win32' else 'auto'
+        backend = 'test' if only_test else 'auto'
     else:
-        if backend != 'test' and sys.platform == 'win32':
-            raise SkipTest('non-testing backend crashes on Windows')
+        if only_test:
+            raise SkipTest('non-testing backend crashes on Windows and '
+                           'Travis Py3k')
     mlab.options.backend = backend
 
 
 @requires_fsaverage
 def test_offscreen():
     """Test offscreen rendering."""
-    if sys.platform == 'darwin' and os.getenv('TRAVIS', 'false') == 'true':
-        raise SkipTest('Offscreen Travis tests fail on OSX')
+    if os.getenv('TRAVIS', 'false') == 'true':
+        if sys.platform == 'darwin':
+            raise SkipTest('Offscreen Travis tests fail on OSX')
+        if sys.version[0] == '3':
+            raise SkipTest('Offscreen Travis tests fail on Py3k')
     _set_backend()
     brain = Brain(*std_args, offscreen=True)
     # Sometimes the first screenshot is rendered with a different
@@ -77,8 +84,7 @@ def test_image():
     brain.save_image(tmp_name)
     brain.save_image(tmp_name, 'rgba', True)
     brain.screenshot()
-    if not (sys.platform.startswith('linux') and
-            os.getenv('TRAVIS', 'false') == 'true'):
+    if not os.getenv('TRAVIS', 'false') == 'true':
         # for some reason these fail on Travis sometimes
         brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
         brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')

surfer/utils.py

@@ -375,7 +375,7 @@ def dec(*args, **kwargs):
             # set it back if we get an exception
             try:
                 ret = function(*args, **kwargs)
-            except:
+            except Exception:
                 set_log_level(old_level)
                 raise
             set_log_level(old_level)

surfer/viz.py

@@ -2260,6 +2260,16 @@ def save_single_image(self, filename, row=-1, col=-1):
         if mlab.options.backend != 'test':
             mlab.savefig(filename, figure=brain._f)
 
+    def _screenshot_figure(self, mode='rgb', antialiased=False, dpi=100):
+        """Create a matplolib figure from the current screenshot."""
+        # adapted from matplotlib.image.imsave
+        from matplotlib.backends.backend_agg import FigureCanvasAgg
+        from matplotlib.figure import Figure
+        fig = Figure(dpi=dpi, frameon=False)  # DPI only used for metadata
+        FigureCanvasAgg(fig)
+        fig.figimage(self.screenshot(mode, antialiased), resize=True)
+        return fig
+
     def save_image(self, filename, mode='rgb', antialiased=False):
         """Save view from all panels to disk
 
@@ -2286,8 +2296,7 @@ def save_image(self, filename, mode='rgb', antialiased=False):
         a Mayavi figure to plot instead of TraitsUI) if you intend to
         script plotting commands.
         """
-        from scipy import misc
-        misc.imsave(filename, self.screenshot(mode, antialiased))
+        self._screenshot_figure(mode, antialiased).savefig(filename)
 
     def screenshot(self, mode='rgb', antialiased=False):
         """Generate a screenshot of current view.
@@ -2643,7 +2652,7 @@ def save_movie(self, fname, time_dilation=4., tmin=None, tmax=None,
             raise ValueError("tmax=%r is greater than the latest time point "
                              "(%r)" % (tmax, self._times[-1]))
         n_frames = floor((tmax - tmin) * time_dilation * framerate)
-        times = np.arange(n_frames)
+        times = np.arange(n_frames, dtype=float)
         times /= framerate * time_dilation
         times += tmin
         interp_func = interp1d(self._times, np.arange(self.n_times))
@@ -3067,10 +3076,6 @@ def _min_diff(self, beg, end):
 
     def _add_scalar_data(self, data):
         """Add scalar values to dataset"""
-        if mlab.options.backend == 'test':
-            # required SetActiveAttribute filter attributes are not set under
-            # the testing backend
-            return 0, self._geo_mesh
         array_id = self._mesh_dataset.point_data.add_array(data)
         self._mesh_dataset.point_data.get_array(array_id).name = array_id
         self._mesh_dataset.point_data.update()
@@ -3088,10 +3093,6 @@ def _add_scalar_data(self, data):
 
     def _remove_scalar_data(self, array_id):
         """Removes scalar data"""
-        if mlab.options.backend == 'test':
-            # required SetActiveAttribute filter attributes are not set under
-            # the testing backend
-            return
         self._mesh_clones.pop(array_id).remove()
         self._mesh_dataset.point_data.remove_array(array_id)
 
@@ -3108,8 +3109,7 @@ def _add_vector_data(self, vectors, vector_values, fmin, fmid, fmax,
 
         # Enable backface culling
         quiver.actor.property.backface_culling = False
-        if mlab.options.backend != 'test':
-            quiver.mlab_source.update()
+        quiver.mlab_source.update()
 
         # Compute scaling for the glyphs
         quiver.glyph.glyph.scale_factor = (scale_factor_norm *
@@ -3336,8 +3336,7 @@ def set_data(self, layer_id, values, vectors=None, vector_values=None):
         self._mesh_dataset.point_data.get_array(
             data['array_id']).from_array(values)
         # avoid "AttributeError: 'Scene' object has no attribute 'update'"
-        if mlab.options.backend != 'test':
-            data['mesh'].update()
+        data['mesh'].update()
         if vectors is not None:
             q = data['glyphs']
 
@@ -3349,8 +3348,7 @@ def set_data(self, layer_id, values, vectors=None, vector_values=None):
             # Update glyphs
             q.mlab_source.vectors = vectors
             q.mlab_source.scalars = vector_values
-            if mlab.options.backend != 'test':
-                q.mlab_source.update()
+            q.mlab_source.update()
 
             # Update changed parameters, and glyph scaling
             q.glyph.glyph.scale_factor = (data['scale_factor_norm'] *