Merge pull request #158 from christianbrodbeck/add_data

[MRG] ENH:  Set initial time in Brain.add_data()

Author: larsoner

examples/plot_meg_inverse_solution.py

@@ -50,23 +50,30 @@ def time_label(t):
     time points (in seconds)
     """
     time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
-                       data.shape[1])
+                       data.shape[1], endpoint=False)
 
     """
     colormap to use
     """
     colormap = 'hot'
 
+    """
+    add data and set the initial time displayed to 100 ms
+    """
     brain.add_data(data, colormap=colormap, vertices=vertices,
                    smoothing_steps=10, time=time, time_label=time_label,
-                   hemi=hemi)
+                   hemi=hemi, initial_time=0.1)
 
 """
-scale colormap and set time (index) to display
+scale colormap
 """
-brain.set_data_time_index(2)
 brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
 
+"""
+To change the time displayed to 80 ms uncomment this line
+"""
+# brain.set_time(0.08)
+
 """
 uncomment these lines to use the interactive TimeViewer GUI
 """

surfer/tests/test_viz.py

@@ -191,16 +191,26 @@ def test_meg_inverse():
     stc = io.read_stc(stc_fname)
     data = stc['data']
     vertices = stc['vertices']
-    time = 1e3 * np.linspace(stc['tmin'],
-                             stc['tmin'] + data.shape[1] * stc['tstep'],
-                             data.shape[1])
+    time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
+                       data.shape[1], endpoint=False)
     colormap = 'hot'
-    time_label = 'time=%0.2f ms'
+
+    def time_label(t):
+        return 'time=%0.2f ms' % (1e3 * t)
+
     brain.add_data(data, colormap=colormap, vertices=vertices,
                    smoothing_steps=10, time=time, time_label=time_label)
-    brain.set_data_time_index(2)
     brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
+    assert_equal(brain.data_dict['lh']['time_idx'], 0)
+
+    brain.set_time(.1)
+    assert_equal(brain.data_dict['lh']['time_idx'], 2)
     # viewer = TimeViewer(brain)
+
+    brain.add_data(data, colormap=colormap, vertices=vertices,
+                   smoothing_steps=10, time=time, time_label=time_label,
+                   initial_time=.09, remove_existing=True)
+    assert_equal(brain.data_dict['lh']['time_idx'], 1)
     brain.close()
 
 

surfer/viz.py

@@ -802,7 +802,8 @@ def add_data(self, array, min=None, max=None, thresh=None,
                  colormap="RdBu_r", alpha=1,
                  vertices=None, smoothing_steps=20, time=None,
                  time_label="time index=%d", colorbar=True,
-                 hemi=None, remove_existing=False, time_label_size=14):
+                 hemi=None, remove_existing=False, time_label_size=14,
+                 initial_time=None):
         """Display data from a numpy array on the surface.
 
         This provides a similar interface to add_overlay, but it displays
@@ -857,6 +858,9 @@ def add_data(self, array, min=None, max=None, thresh=None,
             conserving memory when displaying different data in a loop.
         time_label_size : int
             Font size of the time label (default 14)
+        initial_time : float | None
+            Time initially shown in the plot. ``None`` to use the first time
+            sample (default).
         """
         hemi = self._check_hemi(hemi)
 
@@ -907,6 +911,12 @@ def add_data(self, array, min=None, max=None, thresh=None,
             if not self.n_times == len(time):
                 raise ValueError('time is not the same length as '
                                  'array.shape[1]')
+            # initial time
+            if initial_time is None:
+                initial_time_index = None
+            else:
+                initial_time_index = self.index_for_time(initial_time)
+            # time label
             if isinstance(time_label, string_types):
                 time_label_fmt = time_label
 
@@ -919,6 +929,7 @@ def time_label(x):
         else:
             self._times = None
             self.n_times = None
+            initial_time_index = None
 
         surfs = []
         bars = []
@@ -938,17 +949,19 @@ def time_label(x):
                                   name="time_label", row=row, col=col,
                                   font_size=time_label_size,
                                   justification='right')
-        self._toggle_render(True, views)
         data['surfaces'] = surfs
         data['colorbars'] = bars
         data['orig_ctable'] = ct
 
         if remove_existing and self.data_dict[hemi] is not None:
             for surf in self.data_dict[hemi]['surfaces']:
                 surf.parent.parent.remove()
-
         self.data_dict[hemi] = data
 
+        if initial_time_index is not None:
+            self.set_data_time_index(initial_time_index)
+        self._toggle_render(True, views)
+
     def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
                        remove_existing=True):
         """Add an annotation file.