FSLEyes no longer treats 'ortho' and 'lightbox' separately - they are

now default perspectives.

fsl/data/strings.py

@@ -868,9 +868,11 @@ melodic = TypeDict({
 })
 
 perspectives = {
-    'default' : 'Default layout',
-    'melodic' : 'Melodic mode',
-    'feat'    : 'FEAT mode',
+    'default'  : 'Default layout',
+    'melodic'  : 'Melodic mode',
+    'feat'     : 'FEAT mode',
+    'ortho'    : 'Plain orthographic',
+    'lightbox' : 'Plain lightbox',
 }
 
 tensor = {

fsl/fsleyes/perspectives.py

@@ -627,4 +627,19 @@ BUILT_IN_PERSPECTIVES = collections.OrderedDict((
                      layout2|name=Panel;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=20;besth=20;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|name=OverlayDisplayToolBar;caption=Display toolbar;state=67382012;dir=1;layer=10;row=0;pos=0;prop=100000;bestw=860;besth=49;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|name=LocationPanel;caption=Location;state=67373052;dir=3;layer=2;row=0;pos=1;prop=98544;bestw=440;besth=109;minw=440;minh=109;maxw=-1;maxh=-1;floatx=2730;floaty=1104;floatw=440;floath=125;notebookid=-1;transparent=255|name=AtlasPanel;caption=Atlases;state=67373052;dir=2;layer=1;row=0;pos=0;prop=98904;bestw=318;besth=84;minw=318;minh=84;maxw=-1;maxh=-1;floatx=1091;floaty=143;floatw=318;floath=100;notebookid=-1;transparent=255|name=OverlayListPanel;caption=Overlay list;state=67373052;dir=3;layer=2;row=0;pos=0;prop=87792;bestw=197;besth=80;minw=197;minh=80;maxw=-1;maxh=-1;floatx=2608;floaty=1116;floatw=197;floath=96;notebookid=-1;transparent=255|name=OrthoToolBar;caption=Ortho view toolbar;state=67382012;dir=1;layer=10;row=1;pos=0;prop=100000;bestw=815;besth=34;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=2072;floaty=80;floatw=824;floath=50;notebookid=-1;transparent=255|name=ClusterPanel;caption=Cluster browser;state=67373052;dir=2;layer=1;row=0;pos=1;prop=114760;bestw=390;besth=96;minw=390;minh=96;maxw=-1;maxh=-1;floatx=3516;floaty=636;floatw=390;floath=112;notebookid=-1;transparent=255|dock_size(5,0,0)=10|dock_size(2,1,0)=566|dock_size(1,10,0)=51|dock_size(1,10,1)=36|dock_size(3,2,0)=130|
                      ;;
                      layout2|name=FigureCanvasWxAgg;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=640;besth=480;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=642|
+                     """)),
+
+    ('ortho',
+     textwrap.dedent("""
+                     OrthoPanel
+                     layout2|name=OrthoPanel 1;caption=Ortho View 1;state=67376064;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=20;besth=20;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=22|
+                     ;syncLocation=True,syncOverlayOrder=True,syncOverlayDisplay=True;layout=horizontal,showLabels=True,bgColour=#000000ff,showCursor=True,showZCanvas=True,cursorColour=#00ff00ff,showColourBar=False,showYCanvas=True,showXCanvas=True,colourBarLocation=top
+                     layout2|name=Panel;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=20;besth=20;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=22|
+                     """)),
+    ('lightbox',
+     textwrap.dedent("""
+                     LightBoxPanel
+                     layout2|name=LightBoxPanel 1;caption=Lightbox View 1;state=67376064;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=20;besth=20;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=22|
+                     ;syncLocation=True,syncOverlayOrder=True,syncOverlayDisplay=True;bgColour=#000000ff,showCursor=True,cursorColour=#00ff00ff,highlightSlice=False,zax=0,showColourBar=False,showGridLines=False,colourBarLocation=top
+                     layout2|name=Panel;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=20;besth=20;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=10|
                      """))))

fsl/tools/fsleyes.py

@@ -47,15 +47,17 @@ def parseArgs(argv):
         add_help=False,
         formatter_class=argparse.RawDescriptionHelpFormatter)
 
+    # TODO Dynamically generate perspective list
+    # in description. To do this, you will need
+    # to make fsl.utils.settings work without a
+    # wx.App (so we can retrieve the perspective
+    # list before the GUI is created).
     name        = 'fsleyes'
     description = textwrap.dedent("""\
         FSLeyes - the FSL image viewer.
         
-        The '--scene' option may be used to:
-        
-          - Specify a single view to open ('ortho' or 'lightbox').
-          - Specify a saved perspective to open (TODO list saved
-            perspectives here).
+        Use the '--scene' option to load a saved perspective (e.g. 'default',
+        'melodic', 'feat', 'ortho', or 'lightbox').
         
         If no '--scene' is specified, the previous layout is restored.
         """)
@@ -195,17 +197,13 @@ def interface(parent, args, ctx):
 
     # If a scene or perspective has not been
     # specified, the default behaviour is to
-    # restore the previous frame layout. And
-    # if a scene is specified, the layout is
-    # not saved on exit.
-
+    # restore the previous frame layout. 
     restore = scene is None
-    save    = scene not in ('ortho', 'lightbox')
 
     status.update('Creating FSLeyes interface...')
     
     frame = fsleyesframe.FSLEyesFrame(
-        parent, overlayList, displayCtx, restore, save)
+        parent, overlayList, displayCtx, restore, True)
 
     # Make sure the new frame is shown
     # before destroying the splash screen
@@ -221,14 +219,10 @@ def interface(parent, args, ctx):
     splashFrame.Update()
     wx.CallLater(250, splashFrame.Close)
 
-    # If a scene is specified, we add
-    # the panel corresponding to the scene.
-    if   args.scene == 'ortho':    frame.addViewPanel(views.OrthoPanel)
-    elif args.scene == 'lightbox': frame.addViewPanel(views.LightBoxPanel)
 
-    # Otherwise, if a perspective has been
-    # specified, we load the perspective
-    elif args.scene is not None:
+    # If a perspective has been specified,
+    # we load the perspective
+    if args.scene is not None:
         perspectives.loadPerspective(frame, args.scene)
 
     # The viewPanel is assumed to be a CanvasPanel 
@@ -247,23 +241,6 @@ def interface(parent, args, ctx):
 
         fsleyes_parseargs.applySceneArgs(
             args, overlayList, displayCtx, viewOpts)
-
-    if args.scene == 'ortho':
-
-        viewPanel  = viewPanels[0]
-        displayCtx = viewPanel.getDisplayContext()
-
-        xcentre = args.xcentre
-        ycentre = args.ycentre
-        zcentre = args.zcentre
-
-        if xcentre is None: xcentre = displayCtx.location.yz
-        if ycentre is None: ycentre = displayCtx.location.xz
-        if zcentre is None: zcentre = displayCtx.location.xy
-
-        viewPanel.getXCanvas().centreDisplayAt(*xcentre)
-        viewPanel.getYCanvas().centreDisplayAt(*ycentre)
-        viewPanel.getZCanvas().centreDisplayAt(*zcentre)
  
     return frame
 

fsl/tools/render.py

@@ -345,9 +345,9 @@ def run(args, context):
         c.bgColour        = sceneOpts.bgColour
         c.renderMode      = sceneOpts.renderMode
         c.resolutionLimit = sceneOpts.resolutionLimit
-        c.sliceSpacing    = sceneOpts.sliceSpacing
         c.nrows           = sceneOpts.nrows
         c.ncols           = sceneOpts.ncols
+        c.sliceSpacing    = sceneOpts.sliceSpacing
         c.zrange          = sceneOpts.zrange
         c.showGridLines   = sceneOpts.showGridLines
         c.highlightSlice  = sceneOpts.highlightSlice