ENH: Use multiple views simultaneously

CHANGES

@@ -1,6 +1,17 @@
 PySurfer Changes
 ================
 
+Version 0.4
+-------------
+
+Enhancements
+~~~~~~~~~~~~
+
+- Display data from both hemispheres simultaneously
+- Display multiple views simultaneously
+- Toggling Mayavi toolbars
+- Use nibabel for IO functions
+
 Version 0.3.1
 -------------
 

bin/pysurfer

@@ -24,10 +24,16 @@ if __name__ == '__main__':
     # boot up mlab/IPython
     if len(sys.argv) > 3:
         subjects_dir = os.environ['SUBJECTS_DIR']
-        surf_file = os.path.join(subjects_dir,
-                                 "%s/surf/%s.%s" % tuple(sys.argv[1:4]))
-        if not os.path.exists(surf_file):
-            sys.exit("ERROR: Could not find %s" % surf_file)
+        if sys.argv[2] in ['both', 'split']:
+            hemi_checks = ['lh', 'rh']
+        else:
+            hemi_checks = [sys.argv[2]]
+        for h in hemi_checks:
+            surf_file = os.path.join(subjects_dir,
+                                     "%s/surf/%s.%s" % (sys.argv[1], h,
+                                                        sys.argv[3]))
+            if not os.path.exists(surf_file):
+                sys.exit("ERROR: Could not find %s" % surf_file)
 
     if not is_ipython:
         # Parse the args so that --help exits back to the shell
@@ -62,10 +68,11 @@ if __name__ == '__main__':
         argdict = args.__dict__
         config_opts = dict([(k, v) for k, v in argdict.items()
                                                 if k in confkeys and v])
+        views = args.views
 
         # Load  up the figure and underlying brain object
         b = Brain(args.subject_id, args.hemi, args.surf, args.curv,
-                  args.title, config_opts=config_opts)
+                  args.title, views=views, config_opts=config_opts)
 
         # Maybe load some morphometry
         if args.morphometry is not None:

doc/conf.py

@@ -45,7 +45,8 @@
 
 # General information about the project.
 project = u'PySurfer'
-copyright = u'2011-2012, Michael Waskom, Alexandre Gramfort, Scott Burns, Martin Luessi'
+copyright = (u'2011-2013, Michael Waskom, Alexandre Gramfort, Scott Burns, '
+             'Martin Luessi, Eric Larson')
 
 # Generate the plots for the gallery
 plot_gallery = True
@@ -222,5 +223,5 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'pysurfer', u'PySurfer Documentation',
-     [u'Michael Waskom, Alexandre Gramfort, Scott Burns'], 1)
+     [u'Michael Waskom, Alexandre Gramfort, Scott Burns, Eric Larson'], 1)
 ]

doc/documentation/config_file.rst

@@ -7,7 +7,7 @@ There are several aspects of how PySurfer looks and behaves that you may
 wish to customize but do not want to have to alter every time you
 instantiate a Brain object or use the command-line interface. To
 facilitate this, PySurfer allows you to set certain options with a
-standard Python config file. 
+standard Python config file.
 
 When a new Brain object is created (either in a script or via the
 command-line), it can read configuration options from one of two places:
@@ -27,9 +27,14 @@ Visual
 
 *size*
     How large the sides of the display window should be (measured in
-    pixels.) The window is always square, so just give one value, and 
-    it will be used for the height and width. (Possible values: any
-    positive number.)
+    pixels.) When using this option, the window will be square, and
+    "size" it will be used for the height and width. (Possible values:
+    any positive number.)
+
+*width* and *height*
+    The size of the window. This is an alternative to size, allowing
+    the width and height to be set independently. (Possible values:
+    any positive number.)
 
 *default_view*
     Which view should be shown at the beginning of a visualization
@@ -49,3 +54,8 @@ Overlay
     provided when calling the :meth:`Brain.add_overlay` method.
     (Possible values: any float, ``robust_max``, ``actual_max``.)
 
+Options
+-------
+*logging_level*
+    Amount of verbosity to use in outputting status messages.
+    (Possible values: ``DEBUG``, ``INFO``, ``WARNING``, ``ERROR``.)

doc/documentation/index.rst

@@ -7,5 +7,6 @@ Documentation
 
    ./command_line
    ./custom_viz
+   ./split_brain
    ./config_file
 

doc/documentation/split_brain.rst

@@ -0,0 +1,48 @@
+.. _split_brain:
+
+Working with a split-screen brain
+=================================
+
+The split-screen view can be activated by using the argument ``hemi='split'``.
+Using this option will put views of the left hemisphere in consecutive
+vertical frames on the left, and views of the right hemisphere in
+consecutive vertical frames on the right. For example, running the following::
+
+    brain = Brain('fsaverage', 'split', 'inflated', views=['lat', 'med'])
+
+Will produce a window with two columns (hemispheres) and two rows (the
+lateral and medial views, respectively), shown below.
+
+.. image:: ../../_static/split_view.png
+
+Adding and displaying data
+--------------------------
+
+Data can be added to either hemisphere using the same functions that are
+normally used, e.g. ``add_data``, ``add_overlay``, ``add_morphometry``.
+The objects are automatically shown on all views of the brain. When
+calling these functions, the ``hemi`` keyword argument can be set to
+``hemi='lh'`` or ``hemi='rh'`` to specify the hemisphere to plot to.
+In some instances (e.g., ``add_morphometry``), if no keyword argument
+is provided, PySurfer will attempt to load data or both hemispheres
+automtically.
+
+Note that the ``show_view`` method accepts arguments for the ``row`` and
+``col`` values, which allow the user to control which ``Brain`` panel
+gets the updated view.
+
+Caveats
+-------
+The multi-view support is available thanks to the capabilities of the
+TraitsUI framework. However, due to some limitations in the implementation
+of TraitsUI, there is no guarantee that a set of scripted commands will
+result in a painted window when the user may think it will. For
+example, making a series of calls to ``brain.add_label()`` followed by
+``brain.save_image('out.png')`` may result in some or all of the labels
+being absent from the saved ``out.png``. While we have implemented some
+workarounds to help prevent this occurrance, we cannot guarantee it will
+work. Thus we recommend that for critical non-interactive plotting (e.g.,
+if scripting figure generation for a paper) only a single view is used
+with ``hemi`` set to ``'lh'``, ``'rh'``, or ``'both'``. This will use a single,
+pure Mayavi window, thereby bypassing TraisUI entirely -- this helps
+guarantee that drawing commands result in updated visual display.

doc/index.rst

@@ -10,14 +10,14 @@ MRI and MEG data.
 
 PySurfer offers both a command-line interface designed to broadly
 replicate Freesurfer's Tksurfer program as well as a Python library
-for writing scripts to efficiently explore complex datasets. 
+for writing scripts to efficiently explore complex datasets.
 
 Contents
 --------
 
 .. toctree::
     :maxdepth: 2
-    
+
     install
     examples/index.rst
     documentation/index.rst
@@ -33,6 +33,8 @@ Scott Burns, Harvard Med. School MGH Martinos Center
 
 Martin Luessi, Harvard Med. School MGH Martinos Center
 
+Eric Larson, University of Washington ILABS
+
 License
 -------
 

doc/sphinxext/gen_rst.py

@@ -148,66 +148,51 @@ def generate_file_rst(fname, target_dir, src_dir, plot_gallery):
     this_template = rst_template
     last_dir = os.path.split(src_dir)[-1]
     # to avoid leading . in file names
-    if last_dir == '.': last_dir = ''
-    else: last_dir += '_'
-    short_fname =  last_dir + fname
+    if last_dir == '.':
+        last_dir = ''
+    else:
+        last_dir += '_'
+    short_fname = last_dir + fname
     src_file = os.path.join(src_dir, fname)
     example_file = os.path.join(target_dir, fname)
     shutil.copyfile(src_file, example_file)
     if plot_gallery and fname.startswith('plot'):
         # generate the plot as png image if file name
         # starts with plot and if it is more recent than an
         # existing image.
-        if not os.path.exists(
-                            os.path.join(target_dir, 'images')):
+        if not os.path.exists(os.path.join(target_dir, 'images')):
             os.makedirs(os.path.join(target_dir, 'images'))
         image_file = os.path.join(target_dir, 'images', image_name)
         if (not os.path.exists(image_file) or
-                os.stat(image_file).st_mtime <=
-                    os.stat(src_file).st_mtime):
+                os.stat(image_file).st_mtime <= os.stat(src_file).st_mtime):
             print 'plotting %s' % fname
             import matplotlib.pyplot as plt
             plt.close('all')
             try:
-                try:
-                    from mayavi import mlab
-                except ImportError:
-                    from enthought.mayavi import mlab
-                mlab.close(all=True)
-            except:
-                pass
-
-            try:
-                execfile(example_file, {'pl' : plt})
-                facecolor = plt.gcf().get_facecolor() # hack to keep black bg
+                brain = None
+                global plt
+                global brain
+                execfile(example_file, globals())
+                facecolor = plt.gcf().get_facecolor()  # hack to keep black bg
                 if facecolor == (0.0, 0.0, 0.0, 1.0):
                     plt.savefig(image_file, facecolor='black')
                 else:
                     plt.savefig(image_file)
 
-                try:
-                    try:
-                        from mayavi import mlab
-                    except ImportError:
-                        from enthought.mayavi import mlab
-
-                    e = mlab.get_engine()
-                    if len(e.scenes) > 0:
-                        mlab.savefig(image_file, size=(400, 400))
-                except:
-                    pass
+                brain.save_image(image_file)
+                brain.close()
 
             except:
-                print 80*'_'
+                print 80 * '_'
                 print '%s is not compiling:' % fname
                 traceback.print_exc()
-                print 80*'_'
+                print 80 * '_'
         this_template = plot_rst_template
 
     docstring, short_desc, end_row = extract_docstring(example_file)
 
-    f = open(os.path.join(target_dir, fname[:-2] + 'rst'),'w')
-    f.write( this_template % locals())
+    f = open(os.path.join(target_dir, fname[:-2] + 'rst'), 'w')
+    f.write(this_template % locals())
     f.flush()
 
 

doc/surfer.cfg

@@ -1,4 +1,6 @@
 [visual]
+width=600
+height=600
 background=black
 cortex=classic
 default_view=lateral

examples/plot_from_volume.py

@@ -12,31 +12,37 @@
 from surfer import Brain, io
 
 """Bring up the visualization"""
-brain = Brain("fsaverage", "lh", "inflated",
+brain = Brain("fsaverage", "split", "inflated", views=['lat', 'med'],
               config_opts=dict(background="white"))
 
 """Project the volume file and return as an array"""
 mri_file = "example_data/resting_corr.nii.gz"
 reg_file = "example_data/register.dat"
-surf_data = io.project_volume_data(mri_file, "lh", reg_file)
+surf_data_lh = io.project_volume_data(mri_file, "lh", reg_file)
+surf_data_rh = io.project_volume_data(mri_file, "rh", reg_file)
 
 """
 You can pass this array to the add_overlay method for
 a typical activation overlay (with thresholding, etc.)
 """
-brain.add_overlay(surf_data, min=.3, max=.7, name="ang_corr")
+brain.add_overlay(surf_data_lh, min=.3, max=.7, name="ang_corr_lh", hemi='lh')
+brain.add_overlay(surf_data_rh, min=.3, max=.7, name="ang_corr_rh", hemi='rh')
 
 """
 You can also pass it to add_data for more control
 over the visualzation. Here we'll plot the whole
 range of correlations
 """
-brain.overlays["ang_corr"].remove()
-brain.add_data(surf_data, -.7, .7, colormap="jet", alpha=.7)
+for overlay in brain.overlays_dict["ang_corr_lh"]:
+    overlay.remove()
+for overlay in brain.overlays_dict["ang_corr_rh"]:
+    overlay.remove()
+brain.add_data(surf_data_lh, -.7, .7, colormap="jet", alpha=.7, hemi='lh')
+brain.add_data(surf_data_rh, -.7, .7, colormap="jet", alpha=.7, hemi='rh')
 
 """
 This overlay represents resting-state correlations with a
 seed in left angular gyrus. Let's plot that seed.
 """
 seed_coords = (-45, -67, 36)
-brain.add_foci(seed_coords, map_surface="white")
+brain.add_foci(seed_coords, map_surface="white", hemi='lh')