From ed998b2cd79a5b00d09d1ba4178631145e5cf37c Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 18 Jun 2015 11:53:45 +0300
Subject: [PATCH 01/24] Layout uses pixels instead of inches.

---
 mne/viz/epochs.py |  5 +++--
 mne/viz/utils.py  | 19 ++++++++-----------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 525438a1761..4486e73ff57 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -555,8 +555,9 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
     fig = figure_nobar(facecolor='w', figsize=size)
     fig.canvas.set_window_title('mne_browse_epochs')
     ax = plt.subplot2grid((10, 15), (0, 1), colspan=13, rowspan=9)
-    ax.annotate(title, xy=(0.5, 1), xytext=(0, ax.get_ylim()[1] + 13),
-                ha='center', va='bottom', size=10, xycoords='axes fraction',
+
+    ax.annotate(fig_title, xy=(0.5, 1), xytext=(0, ax.get_ylim()[1] + 15),
+                ha='center', va='bottom', size=12, xycoords='axes fraction',
                 textcoords='offset points')
 
     ax.axis([0, duration, 0, 200])
diff --git a/mne/viz/utils.py b/mne/viz/utils.py
index c1514cd704e..f778756c928 100644
--- a/mne/viz/utils.py
+++ b/mne/viz/utils.py
@@ -270,17 +270,14 @@ def _draw_proj_checkbox(event, params, draw_current_state=True):
 
 def _layout_figure(params, platform=None):
     """Aux function for setting figure layout"""
-    size = params['fig'].get_size_inches()
-    scroll_width = 0.33
-    if platform is None or platform == "linux" or platform == "linux2":
-        hscroll_dist = 0.33
-    else:
-        hscroll_dist = 0.8
-    vscroll_dist = 0.1
-    l_border = 1.2
-    r_border = 0.1
-    t_border = 0.33
-    b_border = 0.5
+    size = params['fig'].get_size_inches() * params['fig'].dpi
+    scroll_width = 25
+    hscroll_dist = 25
+    vscroll_dist = 10
+    l_border = 100
+    r_border = 10
+    t_border = 35
+    b_border = 40
 
     # only bother trying to reset layout if it's reasonable to do so
     if size[0] < 2 * scroll_width or size[1] < 2 * scroll_width + hscroll_dist:

From 7d4e87ced3896dc4f31c0eadc5d9b769a0007f53 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 18 Jun 2015 11:55:57 +0300
Subject: [PATCH 02/24] Removed unused param.

---
 mne/viz/epochs.py | 3 +--
 mne/viz/utils.py  | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 4486e73ff57..81a7498c9bf 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -13,7 +13,6 @@
 from collections import deque
 from functools import partial
 import copy
-from sys import platform
 
 import numpy as np
 
@@ -1358,4 +1357,4 @@ def _close_event(event, params):
 
 def _resize_event(event, params):
     """Function to handle resize event"""
-    _layout_figure(params, platform)
+    _layout_figure(params)
diff --git a/mne/viz/utils.py b/mne/viz/utils.py
index f778756c928..57bc42ae443 100644
--- a/mne/viz/utils.py
+++ b/mne/viz/utils.py
@@ -268,7 +268,7 @@ def _draw_proj_checkbox(event, params, draw_current_state=True):
         pass
 
 
-def _layout_figure(params, platform=None):
+def _layout_figure(params):
     """Aux function for setting figure layout"""
     size = params['fig'].get_size_inches() * params['fig'].dpi
     scroll_width = 25

From 864fda008cb3214c6c4de969f34ded61cae9ad43 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Sun, 21 Jun 2015 14:22:34 +0300
Subject: [PATCH 03/24] Rebase

---
 doc/source/whats_new.rst |  5 +++++
 mne/viz/epochs.py        | 35 +++++++++++++++++++++++++++++++++++
 mne/viz/utils.py         |  8 +++++++-
 3 files changed, 47 insertions(+), 1 deletion(-)

diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst
index 2d81023b71d..9057dee46cc 100644
--- a/doc/source/whats_new.rst
+++ b/doc/source/whats_new.rst
@@ -16,6 +16,8 @@ Changelog
 
     - Speed up zero-phase overlap-add (default) filtering by a factor of up to 2 using linearity by `Ross Maddox`_ and `Eric Larson`_
 
+    - Add support for scaling and adjusting the number of channels/time per view by `Jaakko Leppakangas`_
+
 
 BUG
 ~~~
@@ -26,8 +28,11 @@ BUG
 
     - Fix FFT filter artifacts when using short windows in overlap-add by `Eric Larson`_
 
+<<<<<<< HEAD
     - Fix picking channels from forward operator could return a channel ordering different from ``info['chs']`` by `Chris Bailey`_
 
+=======
+>>>>>>> Rebase
 .. _changes_0_9:
 
 Version 0.9
diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 81a7498c9bf..82a264b19fb 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -650,6 +650,11 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
     text = ax.text(0, 0, 'blank', zorder=2, verticalalignment='baseline',
                    horizontalalignment='left', fontweight='bold')
     text.set_visible(False)
+
+    ax_help_button = plt.subplot2grid((10, 15), (0, 14))
+    help_button = mpl.widgets.Button(ax_help_button, 'Help')
+    help_button.on_clicked(_onclick_help)
+
     params = {'fig': fig,
               'ax': ax,
               'ax2': ax2,
@@ -688,6 +693,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
               'vertline_t': vertline_t,
               'butterfly': False,
               'text': text}
+              'ax_help_button': ax_help_button}
 
     if len(projs) > 0 and not epochs.proj:
         ax_button = plt.subplot2grid((10, 15), (9, 14))
@@ -1358,3 +1364,32 @@ def _close_event(event, params):
 def _resize_event(event, params):
     """Function to handle resize event"""
     _layout_figure(params)
+
+
+def _onclick_help(event):
+    """Function for drawing help window"""
+    import matplotlib.pyplot as plt
+    text = 'left arrow : Navigate left\n'\
+           'right arrow : Navigate right\n'\
+           'down arrow : Navigate channels down\n'\
+           'up arrow : Navigate channels up\n'\
+           '- : Scale down\n'\
+           '+ : Scale up\n'\
+           '= : Scale up\n'\
+           'home : Reduce the number of epochs per view\n'\
+           'end : Increase the number of epochs per view\n'\
+           'page down : Reduce the number of channels per view\n'\
+           'page up : Increase the number of channels per view\n'\
+           'b : Toggle butterfly plot on/off\n'
+    width = 10
+    height = 0.2 * 15
+    fig_help = figure_nobar(figsize=(width, height))
+    fig_help.canvas.set_window_title('Help')
+    plt.axis('off')
+    plt.text(0, 0, text)
+    # this should work for non-test cases
+    try:
+        fig_help.canvas.draw()
+        fig_help.show()
+    except Exception:
+        pass
diff --git a/mne/viz/utils.py b/mne/viz/utils.py
index 57bc42ae443..668e20ac3d3 100644
--- a/mne/viz/utils.py
+++ b/mne/viz/utils.py
@@ -269,7 +269,7 @@ def _draw_proj_checkbox(event, params, draw_current_state=True):
 
 
 def _layout_figure(params):
-    """Aux function for setting figure layout"""
+    """Function for setting figure layout. Shared with raw and epoch plots"""
     size = params['fig'].get_size_inches() * params['fig'].dpi
     scroll_width = 25
     hscroll_dist = 25
@@ -298,6 +298,8 @@ def _layout_figure(params):
     ax_height = 1.0 - ax_y - t_border
 
     pos = [l_border, ax_y, ax_width, ax_height]
+
+    params['ax'].set_position(pos)
     if 'ax2' in params:
         params['ax2'].set_position(pos)
     params['ax'].set_position(pos)
@@ -313,6 +315,10 @@ def _layout_figure(params):
         pos = [l_border + ax_width + vscroll_dist, b_border,
                scroll_width_x, scroll_width_y]
         params['ax_button'].set_position(pos)
+    if 'ax_help_button' in params:
+        pos = [l_border - vscroll_dist - scroll_width_x * 2, b_border,
+               scroll_width_x * 2, scroll_width_y]
+        params['ax_help_button'].set_position(pos)
     params['fig'].canvas.draw()
 
 

From 2a54e7b2948a699b265e67e7ac2da82658503c17 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Sun, 21 Jun 2015 14:17:54 +0300
Subject: [PATCH 04/24] Small fixes.

---
 mne/viz/epochs.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 82a264b19fb..6c18c6b6080 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -568,9 +568,13 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
     ax_hscroll.set_xlabel('Epochs')
     ax_vscroll = plt.subplot2grid((10, 15), (0, 14), rowspan=9)
     ax_vscroll.set_axis_off()
-
     ax_vscroll.add_patch(mpl.patches.Rectangle((0, 0), 1, len(picks),
                                                facecolor='w', zorder=2))
+
+    ax_help_button = plt.subplot2grid((10, 15), (9, 0), colspan=1)
+    help_button = mpl.widgets.Button(ax_help_button, 'Help')
+    help_button.on_clicked(_onclick_help)
+
     # populate vertical and horizontal scrollbars
     for ci in range(len(picks)):
         ax_vscroll.add_patch(mpl.patches.Rectangle((0, ci), 1, 1,
@@ -651,10 +655,6 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
                    horizontalalignment='left', fontweight='bold')
     text.set_visible(False)
 
-    ax_help_button = plt.subplot2grid((10, 15), (0, 14))
-    help_button = mpl.widgets.Button(ax_help_button, 'Help')
-    help_button.on_clicked(_onclick_help)
-
     params = {'fig': fig,
               'ax': ax,
               'ax2': ax2,

From 9ef1b90a83c874b1424bc30febee60994b15521d Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Tue, 23 Jun 2015 16:17:40 +0300
Subject: [PATCH 05/24] Added options for adjusting epochs/channels.

---
 mne/viz/epochs.py | 81 +++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 79 insertions(+), 2 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 6c18c6b6080..dc32e6e7ca3 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -692,8 +692,9 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
               'vert_lines': list(),
               'vertline_t': vertline_t,
               'butterfly': False,
-              'text': text}
-              'ax_help_button': ax_help_button}
+              'text': text,
+              'ax_help_button': ax_help_button,
+              'fig_options': None}
 
     if len(projs) > 0 and not epochs.proj:
         ax_button = plt.subplot2grid((10, 15), (9, 14))
@@ -1240,6 +1241,9 @@ def _plot_onkey(event, params):
         n_times = len(params['epochs'].times)
         if n_times * n_epochs > len(params['data'][0]):
             return
+        if params['t_start'] + n_times * n_epochs > len(params['data'][0]):
+            params['t_start'] -= n_times
+            params['hsel_patch'].set_x(params['t_start'])
         ticks = params['epoch_times'] + 0.5 * n_times
         params['ax2'].set_xticks(ticks[:n_epochs])
         params['n_epochs'] = n_epochs
@@ -1257,6 +1261,8 @@ def _plot_onkey(event, params):
     elif event.key == 'b':
         _prepare_butterfly(params)
         _plot_traces(params)
+    elif event.key == 'i':
+        _open_options(params)
     elif event.key == 'escape':
         plt.close(params['fig'])
 
@@ -1393,3 +1399,74 @@ def _onclick_help(event):
         fig_help.show()
     except Exception:
         pass
+
+
+def _update_epochs(params, n_epochs):
+    """Function for changing the amount of epochs per view."""
+    n_times = len(params['epochs'].times)
+    ticks = params['epoch_times'] + 0.5 * n_times
+    params['ax2'].set_xticks(ticks[:n_epochs])
+    params['n_epochs'] = n_epochs
+    params['duration'] = n_times * n_epochs
+    params['hsel_patch'].set_width(params['duration'])
+    if params['t_start'] + n_times * n_epochs > len(params['data'][0]):
+        params['t_start'] = len(params['data'][0]) - n_times * n_epochs
+        params['hsel_patch'].set_x(params['t_start'])
+
+
+def _update_channels(params, n_channels):
+    """Function for changing the amount of channels per view."""
+    from matplotlib.collections import LineCollection
+    offset = params['ax'].get_ylim()[0] / n_channels
+    params['offsets'] = np.arange(n_channels) * offset + (offset / 2.)
+    while len(params['lines']) > n_channels:
+        params['ax'].collections.pop()
+        params['lines'].pop()
+    while len(params['lines']) < n_channels:
+        lc = LineCollection(list(), linewidths=0.5, zorder=3)
+        params['ax'].add_collection(lc)
+        params['lines'].append(lc)
+    params['ax'].set_yticks(params['offsets'])
+    params['vsel_patch'].set_height(n_channels)
+    params['n_channels'] = n_channels
+
+
+def _open_options(params):
+    """Function for opening the option window."""
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    if params['fig_options'] is not None:
+        # turn off options dialog
+        plt.close(params['fig_options'])
+        params['fig_options'] = None
+        return
+    width = 10
+    height = 7.5
+    params['fig_options'] = figure_nobar(figsize=(width, height))
+    ax_color = 'lightgoldenrodyellow'
+    ax_channels = plt.axes([0.25, 0.1, 0.65, 0.2], axisbg=ax_color)
+    ax_epochs = plt.axes([0.25, 0.35, 0.65, 0.2], axisbg=ax_color)
+    channel_slider = mpl.widgets.Slider(ax_channels, 'Channels', 1,
+                                        len(params['ch_names']),
+                                        valfmt='%0.0f',
+                                        valinit=params['n_channels'])
+    epoch_slider = mpl.widgets.Slider(ax_epochs, 'Epochs', 1,
+                                      len(params['epoch_times']),
+                                      valfmt='%0.0f',
+                                      valinit=params['n_epochs'])
+
+    def update_epochs(val):
+        _update_epochs(params, int(np.around(epoch_slider.val)))
+        _plot_traces(params)
+
+    def update_channels(val):
+        _update_channels(params, int(np.around(channel_slider.val)))
+        _plot_traces(params)
+
+    channel_slider.on_changed(update_channels)
+    epoch_slider.on_changed(update_epochs)
+    try:
+        params['fig_options'].canvas.draw()
+        params['fig_options'].show()
+    except Exception:
+        pass

From 1c9e0e309f1aee01cb54e3901781da43fc7e6af1 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 11:27:59 +0300
Subject: [PATCH 06/24] Update button to options.

---
 mne/viz/epochs.py | 68 ++++++++++++++++++++++-------------------------
 1 file changed, 32 insertions(+), 36 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index dc32e6e7ca3..3810b34333b 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1401,22 +1401,11 @@ def _onclick_help(event):
         pass
 
 
-def _update_epochs(params, n_epochs):
-    """Function for changing the amount of epochs per view."""
-    n_times = len(params['epochs'].times)
-    ticks = params['epoch_times'] + 0.5 * n_times
-    params['ax2'].set_xticks(ticks[:n_epochs])
-    params['n_epochs'] = n_epochs
-    params['duration'] = n_times * n_epochs
-    params['hsel_patch'].set_width(params['duration'])
-    if params['t_start'] + n_times * n_epochs > len(params['data'][0]):
-        params['t_start'] = len(params['data'][0]) - n_times * n_epochs
-        params['hsel_patch'].set_x(params['t_start'])
-
-
-def _update_channels(params, n_channels):
+def _update_channels_epochs(event, params):
     """Function for changing the amount of channels per view."""
     from matplotlib.collections import LineCollection
+    # Channels
+    n_channels = int(np.around(params['channel_slider'].val))
     offset = params['ax'].get_ylim()[0] / n_channels
     params['offsets'] = np.arange(n_channels) * offset + (offset / 2.)
     while len(params['lines']) > n_channels:
@@ -1430,6 +1419,19 @@ def _update_channels(params, n_channels):
     params['vsel_patch'].set_height(n_channels)
     params['n_channels'] = n_channels
 
+    # Epochs
+    n_epochs = int(np.around(params['epoch_slider'].val))
+    n_times = len(params['epochs'].times)
+    ticks = params['epoch_times'] + 0.5 * n_times
+    params['ax2'].set_xticks(ticks[:n_epochs])
+    params['n_epochs'] = n_epochs
+    params['duration'] = n_times * n_epochs
+    params['hsel_patch'].set_width(params['duration'])
+    if params['t_start'] + n_times * n_epochs > len(params['data'][0]):
+        params['t_start'] = len(params['data'][0]) - n_times * n_epochs
+        params['hsel_patch'].set_x(params['t_start'])
+    _plot_traces(params)
+
 
 def _open_options(params):
     """Function for opening the option window."""
@@ -1441,30 +1443,24 @@ def _open_options(params):
         params['fig_options'] = None
         return
     width = 10
-    height = 7.5
+    height = 5
     params['fig_options'] = figure_nobar(figsize=(width, height))
     ax_color = 'lightgoldenrodyellow'
-    ax_channels = plt.axes([0.25, 0.1, 0.65, 0.2], axisbg=ax_color)
-    ax_epochs = plt.axes([0.25, 0.35, 0.65, 0.2], axisbg=ax_color)
-    channel_slider = mpl.widgets.Slider(ax_channels, 'Channels', 1,
-                                        len(params['ch_names']),
-                                        valfmt='%0.0f',
-                                        valinit=params['n_channels'])
-    epoch_slider = mpl.widgets.Slider(ax_epochs, 'Epochs', 1,
-                                      len(params['epoch_times']),
-                                      valfmt='%0.0f',
-                                      valinit=params['n_epochs'])
-
-    def update_epochs(val):
-        _update_epochs(params, int(np.around(epoch_slider.val)))
-        _plot_traces(params)
-
-    def update_channels(val):
-        _update_channels(params, int(np.around(channel_slider.val)))
-        _plot_traces(params)
-
-    channel_slider.on_changed(update_channels)
-    epoch_slider.on_changed(update_epochs)
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.2], axisbg=ax_color)
+    ax_epochs = plt.axes([0.15, 0.35, 0.65, 0.2], axisbg=ax_color)
+    ax_button = plt.axes([0.85, 0.1, 0.1, 0.4])
+    params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
+    params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,
+                                                  len(params['ch_names']),
+                                                  valfmt='%0.0f',
+                                                  valinit=params['n_channels'])
+    params['epoch_slider'] = mpl.widgets.Slider(ax_epochs, 'Epochs', 1,
+                                                len(params['epoch_times']),
+                                                valfmt='%0.0f',
+                                                valinit=params['n_epochs'])
+
+    update = partial(_update_channels_epochs, params=params)
+    params['update_button'].on_clicked(update)
     try:
         params['fig_options'].canvas.draw()
         params['fig_options'].show()

From f69c1e033d80a4e30d9ba716a951edbfaa243d10 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 14:25:14 +0300
Subject: [PATCH 07/24] Infobox layout.

---
 mne/viz/epochs.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 3810b34333b..cdf6f5303e8 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1443,12 +1443,14 @@ def _open_options(params):
         params['fig_options'] = None
         return
     width = 10
-    height = 5
-    params['fig_options'] = figure_nobar(figsize=(width, height))
+    height = 1
+    fig_options = figure_nobar(figsize=(width, height))
+    fig_options.canvas.set_window_title('Viewport dimensions')
+    params['fig_options'] = fig_options
     ax_color = 'lightgoldenrodyellow'
-    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.2], axisbg=ax_color)
-    ax_epochs = plt.axes([0.15, 0.35, 0.65, 0.2], axisbg=ax_color)
-    ax_button = plt.axes([0.85, 0.1, 0.1, 0.4])
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.4], axisbg=ax_color)
+    ax_epochs = plt.axes([0.15, 0.55, 0.65, 0.4], axisbg=ax_color)
+    ax_button = plt.axes([0.85, 0.1, 0.1, 0.85])
     params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
     params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,
                                                   len(params['ch_names']),

From a270e601595b377f1c9d2c6f60ad378b21bfa3c3 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 15:01:05 +0300
Subject: [PATCH 08/24] Updated help.

---
 mne/viz/epochs.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index cdf6f5303e8..c3460b32d6f 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -555,7 +555,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
     fig.canvas.set_window_title('mne_browse_epochs')
     ax = plt.subplot2grid((10, 15), (0, 1), colspan=13, rowspan=9)
 
-    ax.annotate(fig_title, xy=(0.5, 1), xytext=(0, ax.get_ylim()[1] + 15),
+    ax.annotate(title, xy=(0.5, 1), xytext=(0, ax.get_ylim()[1] + 15),
                 ha='center', va='bottom', size=12, xycoords='axes fraction',
                 textcoords='offset points')
 
@@ -1259,10 +1259,16 @@ def _plot_onkey(event, params):
         params['hsel_patch'].set_width(params['duration'])
         _plot_traces(params)
     elif event.key == 'b':
+        if params['fig_options'] is not None:
+            plt.close(params['fig_options'])
+            params['fig_options'] = None
         _prepare_butterfly(params)
         _plot_traces(params)
-    elif event.key == 'i':
-        _open_options(params)
+    elif event.key == 'o':
+        if not params['butterfly']:
+            _open_options(params)
+    elif event.key == '?':
+        _onclick_help(event)
     elif event.key == 'escape':
         plt.close(params['fig'])
 
@@ -1386,9 +1392,13 @@ def _onclick_help(event):
            'end : Increase the number of epochs per view\n'\
            'page down : Reduce the number of channels per view\n'\
            'page up : Increase the number of channels per view\n'\
-           'b : Toggle butterfly plot on/off\n'
-    width = 10
-    height = 0.2 * 15
+           'b : Toggle butterfly plot on/off\n'\
+           'o : Open dialog for adjusting viewport dimensions\n'\
+           'f11 : Toggle full screen mode\n'\
+           '? : Open help box'\
+           'esc : Close mne_browse_epochs\n'
+    width = 8
+    height = 0.25 * 15  # 15 rows of text
     fig_help = figure_nobar(figsize=(width, height))
     fig_help.canvas.set_window_title('Help')
     plt.axis('off')
@@ -1412,7 +1422,8 @@ def _update_channels_epochs(event, params):
         params['ax'].collections.pop()
         params['lines'].pop()
     while len(params['lines']) < n_channels:
-        lc = LineCollection(list(), linewidths=0.5, zorder=3)
+        lc = LineCollection(list(), linewidths=0.5, antialiased=False,
+                            zorder=2, picker=3.)
         params['ax'].add_collection(lc)
         params['lines'].append(lc)
     params['ax'].set_yticks(params['offsets'])

From 2a208dbaaebab613d08d55f005ea6ed438491ed7 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 15:38:05 +0300
Subject: [PATCH 09/24] Changed to hard coded dpi. Updated help. Fig size is
 saved.

---
 mne/viz/epochs.py | 31 +++++++++++++++++++------------
 mne/viz/raw.py    |  2 +-
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index c3460b32d6f..c6dad4cf449 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -16,7 +16,7 @@
 
 import numpy as np
 
-from ..utils import create_chunks, verbose, get_config, deprecated
+from ..utils import create_chunks, verbose, get_config, deprecated, set_config
 from ..io.pick import pick_types, channel_type
 from ..io.proj import setup_proj
 from ..fixes import Counter, _in1d
@@ -551,7 +551,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
         title = epochs.name
         if epochs.name is None or len(title) == 0:
             title = ''
-    fig = figure_nobar(facecolor='w', figsize=size)
+    fig = figure_nobar(facecolor='w', figsize=size, dpi=80)
     fig.canvas.set_window_title('mne_browse_epochs')
     ax = plt.subplot2grid((10, 15), (0, 1), colspan=13, rowspan=9)
 
@@ -1375,13 +1375,16 @@ def _close_event(event, params):
 
 def _resize_event(event, params):
     """Function to handle resize event"""
+    size = ','.join([str(s) for s in params['fig'].get_size_inches()])
+    set_config('MNE_BROWSE_RAW_SIZE', size)
     _layout_figure(params)
 
 
 def _onclick_help(event):
     """Function for drawing help window"""
     import matplotlib.pyplot as plt
-    text = 'left arrow : Navigate left\n'\
+    text = 'Hotkeys:\n\n'\
+           'left arrow : Navigate left\n'\
            'right arrow : Navigate right\n'\
            'down arrow : Navigate channels down\n'\
            'up arrow : Navigate channels up\n'\
@@ -1395,11 +1398,16 @@ def _onclick_help(event):
            'b : Toggle butterfly plot on/off\n'\
            'o : Open dialog for adjusting viewport dimensions\n'\
            'f11 : Toggle full screen mode\n'\
-           '? : Open help box'\
-           'esc : Close mne_browse_epochs\n'
+           '? : Open help box\n'\
+           'esc : Close mne_browse_epochs\n\n'\
+           'Left click on an epoch marks bad epoch to be dropped\n'\
+           'Right click on main axes draws a vertical line on the plot\n'\
+           'Middle click on a line shows the channel name\n'\
+           'Mouse click on the channel name marks a bad channel\n'\
+
     width = 8
-    height = 0.25 * 15  # 15 rows of text
-    fig_help = figure_nobar(figsize=(width, height))
+    height = 0.25 * 21  # 21 rows of text
+    fig_help = figure_nobar(figsize=(width, height), dpi=80)
     fig_help.canvas.set_window_title('Help')
     plt.axis('off')
     plt.text(0, 0, text)
@@ -1412,7 +1420,7 @@ def _onclick_help(event):
 
 
 def _update_channels_epochs(event, params):
-    """Function for changing the amount of channels per view."""
+    """Function for changing the amount of channels and epochs per view."""
     from matplotlib.collections import LineCollection
     # Channels
     n_channels = int(np.around(params['channel_slider'].val))
@@ -1455,12 +1463,11 @@ def _open_options(params):
         return
     width = 10
     height = 1
-    fig_options = figure_nobar(figsize=(width, height))
+    fig_options = figure_nobar(figsize=(width, height), dpi=80)
     fig_options.canvas.set_window_title('Viewport dimensions')
     params['fig_options'] = fig_options
-    ax_color = 'lightgoldenrodyellow'
-    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.4], axisbg=ax_color)
-    ax_epochs = plt.axes([0.15, 0.55, 0.65, 0.4], axisbg=ax_color)
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.4])
+    ax_epochs = plt.axes([0.15, 0.55, 0.65, 0.4])
     ax_button = plt.axes([0.85, 0.1, 0.1, 0.85])
     params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
     params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,
diff --git a/mne/viz/raw.py b/mne/viz/raw.py
index 24e8e1ab2a2..92a343b5e59 100644
--- a/mne/viz/raw.py
+++ b/mne/viz/raw.py
@@ -535,7 +535,7 @@ def plot_raw(raw, events=None, duration=10.0, start=0.0, n_channels=None,
         size = size.split(',')
         size = tuple([float(s) for s in size])
         # have to try/catch when there's no toolbar
-    fig = figure_nobar(facecolor=bgcolor, figsize=size)
+    fig = figure_nobar(facecolor=bgcolor, figsize=size, dpi=80)
     fig.canvas.set_window_title('mne_browse_raw')
     ax = plt.subplot2grid((10, 10), (0, 0), colspan=9, rowspan=9)
     ax.set_title(title, fontsize=12)

From 225c0d4905744ed9e54eb154c0d2ec9b842e8dfc Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 15:58:38 +0300
Subject: [PATCH 10/24] Added message to notify of bad channels.

---
 mne/viz/epochs.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index c6dad4cf449..4e40fb8d243 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -17,6 +17,7 @@
 import numpy as np
 
 from ..utils import create_chunks, verbose, get_config, deprecated, set_config
+from ..utils import logger
 from ..io.pick import pick_types, channel_type
 from ..io.proj import setup_proj
 from ..fixes import Counter, _in1d
@@ -1371,6 +1372,7 @@ def _onpick(event, params):
 def _close_event(event, params):
     """Function to drop selected bad epochs. Called on closing of the plot."""
     params['epochs'].drop_epochs(params['bads'])
+    logger.info('Channels marked as bad: %s' % params['epochs'].info['bads'])
 
 
 def _resize_event(event, params):

From 09763b0798abe30c47fd0f04bb1d10ecb2340bce Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 24 Jun 2015 16:05:57 +0300
Subject: [PATCH 11/24] Small fix to docs.

---
 mne/viz/raw.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/viz/raw.py b/mne/viz/raw.py
index 92a343b5e59..753c910a126 100644
--- a/mne/viz/raw.py
+++ b/mne/viz/raw.py
@@ -350,7 +350,7 @@ def plot_raw(raw, events=None, duration=10.0, start=0.0, n_channels=None,
     color : dict | color object | None
         Color for the data traces. If None, defaults to::
 
-            dict(mag='darkblue', grad='b', eeg='k', eog='k', ecg='r',
+            dict(mag='darkblue', grad='b', eeg='k', eog='k', ecg='m',
                  emg='k', ref_meg='steelblue', misc='k', stim='k',
                  resp='k', chpi='k')
 

From da6bfd8555817e8387faf6ef53a9b35528a42e42 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 25 Jun 2015 12:30:11 +0300
Subject: [PATCH 12/24] Mods to help dialog. Tests.

---
 mne/viz/epochs.py            | 78 ++++++++++++++++++++++++------------
 mne/viz/tests/test_epochs.py |  2 +
 2 files changed, 54 insertions(+), 26 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 4e40fb8d243..8e9aaa60f72 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1,6 +1,6 @@
 """Functions to plot epochs data
 """
-from __future__ import print_function
+from __future__ import print_function, unicode_literals
 
 # Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
 #          Denis Engemann <denis.engemann@gmail.com>
@@ -1385,34 +1385,60 @@ def _resize_event(event, params):
 def _onclick_help(event):
     """Function for drawing help window"""
     import matplotlib.pyplot as plt
-    text = 'Hotkeys:\n\n'\
-           'left arrow : Navigate left\n'\
-           'right arrow : Navigate right\n'\
-           'down arrow : Navigate channels down\n'\
-           'up arrow : Navigate channels up\n'\
-           '- : Scale down\n'\
-           '+ : Scale up\n'\
-           '= : Scale up\n'\
-           'home : Reduce the number of epochs per view\n'\
-           'end : Increase the number of epochs per view\n'\
-           'page down : Reduce the number of channels per view\n'\
-           'page up : Increase the number of channels per view\n'\
-           'b : Toggle butterfly plot on/off\n'\
-           'o : Open dialog for adjusting viewport dimensions\n'\
-           'f11 : Toggle full screen mode\n'\
-           '? : Open help box\n'\
-           'esc : Close mne_browse_epochs\n\n'\
-           'Left click on an epoch marks bad epoch to be dropped\n'\
-           'Right click on main axes draws a vertical line on the plot\n'\
-           'Middle click on a line shows the channel name\n'\
-           'Mouse click on the channel name marks a bad channel\n'\
-
-    width = 8
-    height = 0.25 * 21  # 21 rows of text
+
+    text = u'\u2190 : \n'\
+           u'\u2192 : \n'\
+           u'\u2193 : \n'\
+           u'\u2191 : \n'\
+           u'- : \n'\
+           u'+ or = : \n'\
+           u'home : \n'\
+           u'end : \n'\
+           u'page down : \n'\
+           u'page up : \n'\
+           u'b : \n'\
+           u'o : \n'\
+           u'F11 : \n'\
+           u'? : \n'\
+           u'esc : \n\n'\
+
+    text2 = 'Navigate left\n'\
+            'Navigate right\n'\
+            'Navigate channels down\n'\
+            'Navigate channels up\n'\
+            'Scale down\n'\
+            'Scale up\n'\
+            'Reduce the number of epochs per view\n'\
+            'Increase the number of epochs per view\n'\
+            'Reduce the number of channels per view\n'\
+            'Increase the number of channels per view\n'\
+            'Toggle butterfly plot on/off\n'\
+            'Open dialog for adjusting viewport\n'\
+            'Toggle full screen mode\n'\
+            'Open help box\n'\
+            'Close mne_browse_epochs\n\n'
+
+    text3 = 'Left click on an epoch marks bad epoch to be dropped\n'\
+            'Right click on main axes draws a vertical line on the plot\n'\
+            'Middle click on a line shows the channel name\n'\
+            'Mouse click on the channel name marks a bad channel\n'
+    width = 5
+    height = 0.25 * 19  # 19 rows of text
+
     fig_help = figure_nobar(figsize=(width, height), dpi=80)
     fig_help.canvas.set_window_title('Help')
+    ax1 = plt.subplot2grid((3, 5), (0, 0), rowspan=2)
+    plt.text(0, 1, text, fontname='STIXGeneral', va='top', weight='bold')
+    ax1.set_title('Keyboard shortcuts', va='bottom', ha='left')
+    plt.axis('off')
+    plt.subplot2grid((3, 5), (0, 1), rowspan=2, colspan=4)
+    plt.text(0, 1, text2, fontname='STIXGeneral', va='top')
     plt.axis('off')
-    plt.text(0, 0, text)
+    plt.subplot2grid((3, 5), (2, 0), colspan=5)
+    plt.text(0, 1, text3, fontname='STIXGeneral', va='top')
+    plt.axis('off')
+
+    tight_layout(fig=fig_help)
     # this should work for non-test cases
     try:
         fig_help.canvas.draw()
diff --git a/mne/viz/tests/test_epochs.py b/mne/viz/tests/test_epochs.py
index 23a12ee43c2..484b9faac7e 100644
--- a/mne/viz/tests/test_epochs.py
+++ b/mne/viz/tests/test_epochs.py
@@ -122,6 +122,8 @@ def test_plot_epochs():
     fig.canvas.key_press_event('b')
     fig.canvas.key_press_event('f11')
     fig.canvas.key_press_event('home')
+    fig.canvas.key_press_event('?')
+    fig.canvas.key_press_event('o')
     fig.canvas.key_press_event('end')
     fig.canvas.resize_event()
     fig.canvas.close_event()  # closing and epoch dropping

From e6e0c0852dc8a560a7f96b98606110a499126b2d Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 25 Jun 2015 15:21:34 +0300
Subject: [PATCH 13/24] Rough version of label toggling.

---
 mne/viz/epochs.py | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 8e9aaa60f72..cdbbcfe4e9e 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -964,8 +964,6 @@ def _plot_traces(params):
                                                1e6 * factor)
         ax.set_yticklabels(labels, fontsize=12, color='black')
     else:
-        if n_channels > 100:
-            tick_list = ['']
         ax.set_yticklabels(tick_list, fontsize=12)
     params['vsel_patch'].set_y(ch_start)
     params['fig'].canvas.draw()
@@ -1098,7 +1096,7 @@ def _plot_onscroll(event, params):
 def _mouse_click(event, params):
     """Function to handle mouse click events."""
     if event.inaxes is None:
-        if params['n_channels'] > 100 or params['butterfly']:
+        if params['butterfly']:
             return
         ax = params['ax']
         ylim = ax.get_ylim()
@@ -1416,7 +1414,7 @@ def _onclick_help(event):
             'Open dialog for adjusting viewport\n'\
             'Toggle full screen mode\n'\
             'Open help box\n'\
-            'Close mne_browse_epochs\n\n'
+            'Quit\n\n'
 
     text3 = 'Left click on an epoch marks bad epoch to be dropped\n'\
             'Right click on main axes draws a vertical line on the plot\n'\
@@ -1480,6 +1478,14 @@ def _update_channels_epochs(event, params):
     _plot_traces(params)
 
 
+def _toggle_labels(label, params):
+    """Function for toggling y labels on/off."""
+    labels = params['ax'].yaxis.get_ticklabels()
+    for label in labels:
+        label.set_visible(not label.get_visible())
+    params['fig'].canvas.draw()
+
+
 def _open_options(params):
     """Function for opening the option window."""
     import matplotlib.pyplot as plt
@@ -1490,13 +1496,15 @@ def _open_options(params):
         params['fig_options'] = None
         return
     width = 10
-    height = 1
+    height = 5
     fig_options = figure_nobar(figsize=(width, height), dpi=80)
     fig_options.canvas.set_window_title('Viewport dimensions')
     params['fig_options'] = fig_options
-    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.4])
-    ax_epochs = plt.axes([0.15, 0.55, 0.65, 0.4])
-    ax_button = plt.axes([0.85, 0.1, 0.1, 0.85])
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.25])
+    ax_epochs = plt.axes([0.15, 0.4, 0.65, 0.25])
+    ax_button = plt.axes([0.85, 0.1, 0.1, 0.55])
+    ax_check = plt.axes([0.15, 0.70, 0.4, 0.25])
+    plt.axis('off')
     params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
     params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,
                                                   len(params['ch_names']),
@@ -1506,9 +1514,14 @@ def _open_options(params):
                                                 len(params['epoch_times']),
                                                 valfmt='%0.0f',
                                                 valinit=params['n_epochs'])
-
+    toggled = params['ax'].yaxis.get_ticklabels()[0].get_visible()
+    params['checkbox'] = mpl.widgets.CheckButtons(ax_check,
+                                                  ['Y labels visible'],
+                                                  actives=[toggled])
     update = partial(_update_channels_epochs, params=params)
     params['update_button'].on_clicked(update)
+    labels_callback = partial(_toggle_labels, params=params)
+    params['checkbox'].on_clicked(labels_callback)
     try:
         params['fig_options'].canvas.draw()
         params['fig_options'].show()

From f63f61425face972b1ba372691b39059bae47ea4 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 25 Jun 2015 16:15:29 +0300
Subject: [PATCH 14/24] Rough version of toggling t0.

---
 mne/viz/epochs.py | 45 +++++++++++++++++++++++++++------------------
 1 file changed, 27 insertions(+), 18 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index cdbbcfe4e9e..ab75793342f 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -695,7 +695,8 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
               'butterfly': False,
               'text': text,
               'ax_help_button': ax_help_button,
-              'fig_options': None}
+              'fig_options': None,
+              't0_visible': True}
 
     if len(projs) > 0 and not epochs.proj:
         ax_button = plt.subplot2grid((10, 15), (9, 14))
@@ -1031,14 +1032,16 @@ def _channels_changed(params):
 def _plot_vert_lines(params):
     """ Helper function for plotting vertical lines."""
     ax = params['ax']
-    ax.lines = list()
+    while len(ax.lines) > 0:
+        ax.lines.pop()
     epochs = params['epochs']
-    t_zero = np.where(epochs.times == 0.)[0]
-    if len(t_zero) == 1:
-        for event_idx in range(len(epochs.events)):
-            pos = [event_idx * len(epochs.times) + t_zero[0],
-                   event_idx * len(epochs.times) + t_zero[0]]
-            ax.plot(pos, ax.get_ylim(), 'g', zorder=3, alpha=0.4)
+    if params['t0_visible']:
+        t_zero = np.where(epochs.times == 0.)[0]
+        if len(t_zero) == 1:
+            for event_idx in range(len(epochs.events)):
+                pos = [event_idx * len(epochs.times) + t_zero[0],
+                       event_idx * len(epochs.times) + t_zero[0]]
+                ax.plot(pos, ax.get_ylim(), 'g', zorder=3, alpha=0.4)
     for epoch_idx in range(len(epochs.events)):
         pos = [epoch_idx * len(epochs.times), epoch_idx * len(epochs.times)]
         ax.plot(pos, ax.get_ylim(), color='black', linestyle='--', zorder=1)
@@ -1480,9 +1483,13 @@ def _update_channels_epochs(event, params):
 
 def _toggle_labels(label, params):
     """Function for toggling y labels on/off."""
-    labels = params['ax'].yaxis.get_ticklabels()
-    for label in labels:
-        label.set_visible(not label.get_visible())
+    if label == 'Y labels visible':
+        labels = params['ax'].yaxis.get_ticklabels()
+        for label in labels:
+            label.set_visible(not label.get_visible())
+    elif label == 'T0 visible':
+        params['t0_visible'] = not params['t0_visible']
+        _plot_vert_lines(params)
     params['fig'].canvas.draw()
 
 
@@ -1500,10 +1507,10 @@ def _open_options(params):
     fig_options = figure_nobar(figsize=(width, height), dpi=80)
     fig_options.canvas.set_window_title('Viewport dimensions')
     params['fig_options'] = fig_options
-    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.25])
-    ax_epochs = plt.axes([0.15, 0.4, 0.65, 0.25])
-    ax_button = plt.axes([0.85, 0.1, 0.1, 0.55])
-    ax_check = plt.axes([0.15, 0.70, 0.4, 0.25])
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.2])
+    ax_epochs = plt.axes([0.15, 0.35, 0.65, 0.2])
+    ax_button = plt.axes([0.85, 0.1, 0.1, 0.45])
+    ax_check = plt.axes([0.15, 0.60, 0.4, 0.35])
     plt.axis('off')
     params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
     params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,
@@ -1514,10 +1521,12 @@ def _open_options(params):
                                                 len(params['epoch_times']),
                                                 valfmt='%0.0f',
                                                 valinit=params['n_epochs'])
-    toggled = params['ax'].yaxis.get_ticklabels()[0].get_visible()
+    actives = [params['ax'].yaxis.get_ticklabels()[0].get_visible(),
+               params['t0_visible']]
     params['checkbox'] = mpl.widgets.CheckButtons(ax_check,
-                                                  ['Y labels visible'],
-                                                  actives=[toggled])
+                                                  ['Y labels visible',
+                                                   'T0 visible'],
+                                                  actives=actives)
     update = partial(_update_channels_epochs, params=params)
     params['update_button'].on_clicked(update)
     labels_callback = partial(_toggle_labels, params=params)

From ad056c7cb032006ce0840cf2d8637b717d276dca Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Thu, 25 Jun 2015 16:31:40 +0300
Subject: [PATCH 15/24] Layout of options.

---
 mne/viz/epochs.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index ab75793342f..eac49fafc20 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1503,14 +1503,14 @@ def _open_options(params):
         params['fig_options'] = None
         return
     width = 10
-    height = 5
+    height = 3
     fig_options = figure_nobar(figsize=(width, height), dpi=80)
     fig_options.canvas.set_window_title('Viewport dimensions')
     params['fig_options'] = fig_options
-    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.2])
-    ax_epochs = plt.axes([0.15, 0.35, 0.65, 0.2])
-    ax_button = plt.axes([0.85, 0.1, 0.1, 0.45])
-    ax_check = plt.axes([0.15, 0.60, 0.4, 0.35])
+    ax_channels = plt.axes([0.15, 0.1, 0.65, 0.1])
+    ax_epochs = plt.axes([0.15, 0.25, 0.65, 0.1])
+    ax_button = plt.axes([0.85, 0.1, 0.1, 0.25])
+    ax_check = plt.axes([0.15, 0.4, 0.4, 0.55])
     plt.axis('off')
     params['update_button'] = mpl.widgets.Button(ax_button, 'Update')
     params['channel_slider'] = mpl.widgets.Slider(ax_channels, 'Channels', 1,

From 45d03a46ab141ba65f8dd8c2933e34b77765df43 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Fri, 26 Jun 2015 11:14:05 +0300
Subject: [PATCH 16/24] Added check boxes. Changes to help.

---
 mne/viz/epochs.py | 68 +++++++++++++++++++++++++++++------------------
 1 file changed, 42 insertions(+), 26 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index eac49fafc20..1680c6795d7 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -696,7 +696,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
               'text': text,
               'ax_help_button': ax_help_button,
               'fig_options': None,
-              't0_visible': True}
+              'settings': [True, True, True, True]}  # for options dialog
 
     if len(projs) > 0 and not epochs.proj:
         ax_button = plt.subplot2grid((10, 15), (9, 14))
@@ -1035,7 +1035,7 @@ def _plot_vert_lines(params):
     while len(ax.lines) > 0:
         ax.lines.pop()
     epochs = params['epochs']
-    if params['t0_visible']:
+    if params['settings'][3]:  # if zeroline visible
         t_zero = np.where(epochs.times == 0.)[0]
         if len(t_zero) == 1:
             for event_idx in range(len(epochs.events)):
@@ -1402,6 +1402,11 @@ def _onclick_help(event):
            u'F11 : \n'\
            u'? : \n'\
            u'esc : \n\n'\
+           u'Mouse controls\n'\
+           u'click epoch :\n'\
+           u'click channel name :\n'\
+           u'right click :\n'\
+           u'middle click :\n'
 
     text2 = 'Navigate left\n'\
             'Navigate right\n'\
@@ -1414,30 +1419,30 @@ def _onclick_help(event):
             'Reduce the number of channels per view\n'\
             'Increase the number of channels per view\n'\
             'Toggle butterfly plot on/off\n'\
-            'Open dialog for adjusting viewport\n'\
+            'View settings (orig. view only)\n'\
             'Toggle full screen mode\n'\
             'Open help box\n'\
-            'Quit\n\n'
+            'Quit\n\n\n'\
+            'Mark bad epoch\n'\
+            'Mark bad channel\n'\
+            'Verticlal line at a time instant\n'\
+            'Show channel name (butterfly plot)\n'
 
-    text3 = 'Left click on an epoch marks bad epoch to be dropped\n'\
-            'Right click on main axes draws a vertical line on the plot\n'\
-            'Middle click on a line shows the channel name\n'\
-            'Mouse click on the channel name marks a bad channel\n'
-    width = 5
+    width = 5.5
     height = 0.25 * 19  # 19 rows of text
 
     fig_help = figure_nobar(figsize=(width, height), dpi=80)
     fig_help.canvas.set_window_title('Help')
-    ax1 = plt.subplot2grid((3, 5), (0, 0), rowspan=2)
-    plt.text(0, 1, text, fontname='STIXGeneral', va='top', weight='bold')
-    ax1.set_title('Keyboard shortcuts', va='bottom', ha='left')
+    ax1 = plt.subplot2grid((1, 5), (0, 0), colspan=2)
+    ax1.set_yticklabels(list())
+    plt.text(0.99, 1, text, fontname='STIXGeneral', va='top', weight='bold',
+             ha='right')
     plt.axis('off')
-    plt.subplot2grid((3, 5), (0, 1), rowspan=2, colspan=4)
+
+    ax2 = plt.subplot2grid((1, 5), (0, 2), colspan=3)
+    ax2.set_yticklabels(list())
     plt.text(0, 1, text2, fontname='STIXGeneral', va='top')
     plt.axis('off')
-    plt.subplot2grid((3, 5), (2, 0), colspan=5)
-    plt.text(0, 1, text3, fontname='STIXGeneral', va='top')
-    plt.axis('off')
 
     tight_layout(fig=fig_help)
     # this should work for non-test cases
@@ -1482,13 +1487,24 @@ def _update_channels_epochs(event, params):
 
 
 def _toggle_labels(label, params):
-    """Function for toggling y labels on/off."""
-    if label == 'Y labels visible':
+    """Function for toggling axis labels on/off."""
+    if label == 'Channel names visible':
+        params['settings'][0] = not params['settings'][0]
         labels = params['ax'].yaxis.get_ticklabels()
         for label in labels:
-            label.set_visible(not label.get_visible())
-    elif label == 'T0 visible':
-        params['t0_visible'] = not params['t0_visible']
+            label.set_visible(params['settings'][0])
+    elif label == 'Event-id visible':
+        params['settings'][1] = not params['settings'][1]
+        labels = params['ax2'].xaxis.get_ticklabels()
+        for label in labels:
+            label.set_visible(params['settings'][1])
+    elif label == 'Epoch-id visible':
+        params['settings'][2] = not params['settings'][2]
+        labels = params['ax'].xaxis.get_ticklabels()
+        for label in labels:
+            label.set_visible(params['settings'][2])
+    elif label == 'Zeroline visible':
+        params['settings'][3] = not params['settings'][3]
         _plot_vert_lines(params)
     params['fig'].canvas.draw()
 
@@ -1521,12 +1537,12 @@ def _open_options(params):
                                                 len(params['epoch_times']),
                                                 valfmt='%0.0f',
                                                 valinit=params['n_epochs'])
-    actives = [params['ax'].yaxis.get_ticklabels()[0].get_visible(),
-               params['t0_visible']]
     params['checkbox'] = mpl.widgets.CheckButtons(ax_check,
-                                                  ['Y labels visible',
-                                                   'T0 visible'],
-                                                  actives=actives)
+                                                  ['Channel names visible',
+                                                   'Event-id visible',
+                                                   'Epoch-id visible',
+                                                   'Zeroline visible'],
+                                                  actives=params['settings'])
     update = partial(_update_channels_epochs, params=params)
     params['update_button'].on_clicked(update)
     labels_callback = partial(_toggle_labels, params=params)

From 4a7a79034e19283393e668cd56372b2b1708791c Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Fri, 26 Jun 2015 12:10:59 +0300
Subject: [PATCH 17/24] Title to help.

---
 mne/viz/epochs.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 1680c6795d7..85cf60d3acd 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1433,13 +1433,16 @@ def _onclick_help(event):
 
     fig_help = figure_nobar(figsize=(width, height), dpi=80)
     fig_help.canvas.set_window_title('Help')
-    ax1 = plt.subplot2grid((1, 5), (0, 0), colspan=2)
+    ax = plt.subplot2grid((8, 5), (0, 0), colspan=5)
+    ax.set_title('Keyboard shortcuts')
+    plt.axis('off')
+    ax1 = plt.subplot2grid((8, 5), (1, 0), rowspan=7, colspan=2)
     ax1.set_yticklabels(list())
     plt.text(0.99, 1, text, fontname='STIXGeneral', va='top', weight='bold',
              ha='right')
     plt.axis('off')
 
-    ax2 = plt.subplot2grid((1, 5), (0, 2), colspan=3)
+    ax2 = plt.subplot2grid((8, 5), (1, 2), rowspan=7, colspan=3)
     ax2.set_yticklabels(list())
     plt.text(0, 1, text2, fontname='STIXGeneral', va='top')
     plt.axis('off')

From f570c2ac91777c63d0aaabc4ff2b59480d9fa215 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Fri, 26 Jun 2015 12:55:53 +0300
Subject: [PATCH 18/24] Small fixes.

---
 mne/viz/epochs.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 85cf60d3acd..592c946beb8 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1,6 +1,5 @@
 """Functions to plot epochs data
 """
-from __future__ import print_function, unicode_literals
 
 # Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
 #          Denis Engemann <denis.engemann@gmail.com>
@@ -1099,7 +1098,7 @@ def _plot_onscroll(event, params):
 def _mouse_click(event, params):
     """Function to handle mouse click events."""
     if event.inaxes is None:
-        if params['butterfly']:
+        if params['butterfly'] or not params['settings'][0]:
             return
         ax = params['ax']
         ylim = ax.get_ylim()
@@ -1286,6 +1285,9 @@ def _prepare_butterfly(params):
             return
         params['ax_vscroll'].set_visible(False)
         ax = params['ax']
+        labels = ax.yaxis.get_ticklabels()
+        for label in labels:
+            label.set_visible(True)
         ylim = (5. * len(types), 0.)
         ax.set_ylim(ylim)
         offset = ylim[0] / (4. * len(types))
@@ -1337,9 +1339,12 @@ def _prepare_butterfly(params):
         while len(params['lines']) < len(params['picks']):
             lc = LineCollection(list(), antialiased=False, linewidths=0.5,
                                 zorder=2, picker=3.)
-            params['ax'].add_collection(lc)
+            ax.add_collection(lc)
             params['lines'].append(lc)
     else:  # change back to default view
+        labels = params['ax'].yaxis.get_ticklabels()
+        for label in labels:
+            label.set_visible(params['settings'][0])
         params['ax_vscroll'].set_visible(True)
         while len(params['ax2'].texts) > 0:
             params['ax2'].texts.pop()
@@ -1524,7 +1529,7 @@ def _open_options(params):
     width = 10
     height = 3
     fig_options = figure_nobar(figsize=(width, height), dpi=80)
-    fig_options.canvas.set_window_title('Viewport dimensions')
+    fig_options.canvas.set_window_title('View settings')
     params['fig_options'] = fig_options
     ax_channels = plt.axes([0.15, 0.1, 0.65, 0.1])
     ax_epochs = plt.axes([0.15, 0.25, 0.65, 0.1])

From e506fd77c9f0f2947255c3eeb1b075f709c00818 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Sat, 27 Jun 2015 12:36:07 +0300
Subject: [PATCH 19/24] Fix attempt.

---
 mne/viz/epochs.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 592c946beb8..ae76c90c056 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1141,6 +1141,8 @@ def _mouse_click(event, params):
 
     elif event.inaxes == params['ax'] and event.button == 2:  # middle click
         params['fig'].canvas.draw()
+        if params['fig_proj'] is not None:
+            params['fig_proj'].canvas.draw()
     elif event.inaxes == params['ax'] and event.button == 3:  # right click
         n_times = len(params['epochs'].times)
         xdata = int(event.xdata % n_times)
@@ -1515,6 +1517,8 @@ def _toggle_labels(label, params):
         params['settings'][3] = not params['settings'][3]
         _plot_vert_lines(params)
     params['fig'].canvas.draw()
+    if params['fig_proj'] is not None:
+        params['fig_proj'].canvas.draw()
 
 
 def _open_options(params):
@@ -1555,8 +1559,17 @@ def _open_options(params):
     params['update_button'].on_clicked(update)
     labels_callback = partial(_toggle_labels, params=params)
     params['checkbox'].on_clicked(labels_callback)
+    close_callback = partial(_settings_closed, params=params)
+    params['fig_options'].canvas.mpl_connect('close_event', close_callback)
     try:
         params['fig_options'].canvas.draw()
         params['fig_options'].show()
+        if params['fig_proj'] is not None:
+            params['fig_proj'].canvas.draw()
     except Exception:
         pass
+
+
+def _settings_closed(events, params):
+    """Function to handle close event from settings dialog."""
+    params['fig_options'] = None

From cf40b7277550210e5d74e11a8f6298437648a8db Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Mon, 29 Jun 2015 08:41:47 +0300
Subject: [PATCH 20/24] Small tweaks.

---
 mne/viz/epochs.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index ae76c90c056..aaf122e5f96 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1400,15 +1400,15 @@ def _onclick_help(event):
            u'\u2191 : \n'\
            u'- : \n'\
            u'+ or = : \n'\
-           u'home : \n'\
-           u'end : \n'\
-           u'page down : \n'\
-           u'page up : \n'\
+           u'Home : \n'\
+           u'End : \n'\
+           u'Page down : \n'\
+           u'Page up : \n'\
            u'b : \n'\
            u'o : \n'\
            u'F11 : \n'\
            u'? : \n'\
-           u'esc : \n\n'\
+           u'Esc : \n\n'\
            u'Mouse controls\n'\
            u'click epoch :\n'\
            u'click channel name :\n'\

From 80a4e66f37908631cad9ff6ca1b1c8e7a923a735 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Tue, 30 Jun 2015 12:41:10 +0300
Subject: [PATCH 21/24] Changed the position of vertical line text field.

---
 mne/viz/epochs.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index aaf122e5f96..b3f87fef0d9 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -628,9 +628,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
     ax2.set_xticklabels(labels)
     xlim = epoch_times[-1] + len(epochs.times)
     ax_hscroll.set_xlim(0, xlim)
-    vertline_t = ax_hscroll.text(0, 0.5, '', color='y',
-                                 verticalalignment='center',
-                                 horizontalalignment='right')
+    vertline_t = ax_hscroll.text(0, 1, '', color='y', va='bottom', ha='right')
 
     # fit horizontal scroll bar ticks
     hscroll_ticks = np.arange(0, xlim, xlim / 7.0)
@@ -652,7 +650,7 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20,
                                        alpha=0.25, linewidth=1, clip_on=False)
     ax_hscroll.add_patch(hsel_patch)
     text = ax.text(0, 0, 'blank', zorder=2, verticalalignment='baseline',
-                   horizontalalignment='left', fontweight='bold')
+                   ha='left', fontweight='bold')
     text.set_visible(False)
 
     params = {'fig': fig,

From 85102c2bc1aa2679c0d67df7baed3ba266bcf23e Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 8 Jul 2015 15:46:23 +0300
Subject: [PATCH 22/24] Clean up.

---
 doc/source/whats_new.rst | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst
index 9057dee46cc..f0ac91cc10d 100644
--- a/doc/source/whats_new.rst
+++ b/doc/source/whats_new.rst
@@ -28,11 +28,8 @@ BUG
 
     - Fix FFT filter artifacts when using short windows in overlap-add by `Eric Larson`_
 
-<<<<<<< HEAD
     - Fix picking channels from forward operator could return a channel ordering different from ``info['chs']`` by `Chris Bailey`_
 
-=======
->>>>>>> Rebase
 .. _changes_0_9:
 
 Version 0.9

From 8f1f5a9cd05da9c376158b5216375151ca234ae4 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 8 Jul 2015 15:52:03 +0300
Subject: [PATCH 23/24] Added empty line.

---
 mne/viz/epochs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index b3f87fef0d9..6a8c381f137 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1571,3 +1571,4 @@ def _open_options(params):
 def _settings_closed(events, params):
     """Function to handle close event from settings dialog."""
     params['fig_options'] = None
+

From 709638e109d09841ddb7bafda8b6483f193d6139 Mon Sep 17 00:00:00 2001
From: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
Date: Wed, 8 Jul 2015 16:38:23 +0300
Subject: [PATCH 24/24] Removed empty line.

---
 mne/viz/epochs.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mne/viz/epochs.py b/mne/viz/epochs.py
index 6a8c381f137..b3f87fef0d9 100644
--- a/mne/viz/epochs.py
+++ b/mne/viz/epochs.py
@@ -1571,4 +1571,3 @@ def _open_options(params):
 def _settings_closed(events, params):
     """Function to handle close event from settings dialog."""
     params['fig_options'] = None
-