RF Brain.save_movie(): use imageio library

Author: christianbrodbeck

setup.py

@@ -92,5 +92,6 @@ def check_dependencies():
           platforms='any',
           packages=['surfer', 'surfer.tests'],
           scripts=['bin/pysurfer'],
-          install_requires=['nibabel >= 1.2'],
+          install_requires=['nibabel >= 1.2',
+                            'imageio >= 1.5'],
           )

surfer/tests/test_viz.py

@@ -1,18 +1,18 @@
-import numpy as np
 import os
 import os.path as op
 from os.path import join as pjoin
-import re
 import shutil
-import subprocess
-from nose.tools import assert_equal
-from numpy.testing import assert_raises, assert_array_equal
 from tempfile import mkdtemp, mktemp
+
+import imageio
+from nose.tools import assert_equal
+from mayavi import mlab
 import nibabel as nib
+import numpy as np
+from numpy.testing import assert_raises, assert_array_equal
 
 from surfer import Brain, io, utils
-from surfer.utils import requires_ffmpeg, requires_fsaverage
-from mayavi import mlab
+from surfer.utils import requires_fsaverage
 
 subj_dir = utils._get_subjects_dir()
 subject_id = 'fsaverage'
@@ -214,7 +214,6 @@ def test_morphometry():
     brain.close()
 
 
-@requires_ffmpeg
 @requires_fsaverage
 def test_movie():
     """Test saving a movie of an MEG inverse solution
@@ -234,18 +233,16 @@ def test_movie():
     tempdir = mkdtemp()
     try:
         dst = os.path.join(tempdir, 'test.mov')
+        # test the number of frames in the movie
         brain.save_movie(dst)
+        frames = imageio.mimread(dst)
+        assert_equal(len(frames), 2)
+        brain.save_movie(dst, time_dilation=10)
+        frames = imageio.mimread(dst)
+        assert_equal(len(frames), 7)
         brain.save_movie(dst, tmin=0.081, tmax=0.102)
-        # test the number of frames in the movie
-        sp = subprocess.Popen(('ffmpeg', '-i', 'test.mov', '-vcodec', 'copy',
-                               '-f', 'null', '/dev/null'), cwd=tempdir,
-                              stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        stdout, stderr = sp.communicate()
-        m = re.search('frame=\s*(\d+)\s', stderr)
-        if not m:
-            raise RuntimeError(stderr)
-        n_frames = int(m.group(1))
-        assert_equal(n_frames, 3)
+        frames = imageio.mimread(dst)
+        assert_equal(len(frames), 2)
     finally:
         # clean up
         shutil.rmtree(tempdir)

surfer/viz.py

@@ -1,9 +1,9 @@
 from math import floor
 import os
 from os.path import join as pjoin
-from tempfile import mkdtemp
 from warnings import warn
 
+import imageio
 import numpy as np
 from scipy import stats, ndimage, misc
 from scipy.interpolate import interp1d
@@ -21,7 +21,7 @@
 
 from . import utils, io
 from .utils import (Surface, verbose, create_color_lut, _get_subjects_dir,
-                    string_types, assert_ffmpeg_is_available, ffmpeg)
+                    string_types)
 
 
 import logging
@@ -730,6 +730,35 @@ def _get_display_range(self, scalar_data, min, max, sign):
 
         return min, max
 
+    def _iter_time(self, time_idx, interpolation):
+        """Iterate through time points, then reset to current time
+
+        Parameters
+        ----------
+        time_idx : array_like
+            Time point indexes through which to iterate.
+        interpolation : str
+            Interpolation method (``scipy.interpolate.interp1d`` parameter,
+            one of 'linear' | 'nearest' | 'zero' | 'slinear' | 'quadratic' |
+            'cubic'). Interpolation is only used for non-integer indexes.
+
+        Yields
+        ------
+        idx : int | float
+            Current index.
+
+        Notes
+        -----
+        Used by movie and image sequence saving functions.
+        """
+        current_time_idx = self.data_time_index
+        for idx in time_idx:
+            self.set_data_time_index(idx, interpolation)
+            yield idx
+
+        # Restore original time index
+        self.set_data_time_index(current_time_idx)
+
     ###########################################################################
     # ADDING DATA PLOTS
     def add_overlay(self, source, min=2, max="robust_max", sign="abs",
@@ -2041,12 +2070,9 @@ def save_image_sequence(self, time_idx, fname_pattern, use_abs_idx=True,
         images_written: list
             all filenames written
         """
-        current_time_idx = self.data_time_index
         images_written = list()
-        rel_pos = 0
-        for idx in time_idx:
-            self.set_data_time_index(idx, interpolation)
-            fname = fname_pattern % (idx if use_abs_idx else rel_pos)
+        for i, idx in enumerate(self._iter_time(time_idx, interpolation)):
+            fname = fname_pattern % (idx if use_abs_idx else i)
             if montage == 'single':
                 self.save_single_image(fname, row, col)
             elif montage == 'current':
@@ -2055,10 +2081,6 @@ def save_image_sequence(self, time_idx, fname_pattern, use_abs_idx=True,
                 self.save_montage(fname, montage, 'h', border_size, colorbar,
                                   row, col)
             images_written.append(fname)
-            rel_pos += 1
-
-        # Restore original time index
-        self.set_data_time_index(current_time_idx)
 
         return images_written
 
@@ -2172,15 +2194,7 @@ def save_movie(self, fname, time_dilation=4., tmin=None, tmax=None,
         bitrate : str | float
             Bitrate to use to encode movie. Can be specified as number (e.g.
             64000) or string (e.g. '64k'). Default value is 1M
-
-        Notes
-        -----
-        This method requires FFmpeg to be installed in the system PATH. FFmpeg
-        is free and can be obtained from `here
-        <http://ffmpeg.org/download.html>`_.
         """
-        assert_ffmpeg_is_available()
-
         if tmin is None:
             tmin = self._times[0]
         elif tmin < self._times[0]:
@@ -2206,12 +2220,10 @@ def save_movie(self, fname, time_dilation=4., tmin=None, tmax=None,
 
         logger.debug("Save movie for time points/samples\n%s\n%s"
                      % (times, time_idx))
-        tempdir = mkdtemp()
-        frame_pattern = 'frame%%0%id.png' % (np.floor(np.log10(n_times)) + 1)
-        fname_pattern = os.path.join(tempdir, frame_pattern)
-        self.save_image_sequence(time_idx, fname_pattern, False, -1, -1,
-                                 'current', interpolation=interpolation)
-        ffmpeg(fname, fname_pattern, framerate, codec=codec, bitrate=bitrate)
+        images = (self.screenshot() for _ in
+                  self._iter_time(time_idx, interpolation))
+        imageio.mimwrite(fname, images, fps=framerate, codec=codec,
+                         bitrate=bitrate)
 
     def animate(self, views, n_steps=180., fname=None, use_cache=False,
                 row=-1, col=-1):