script updates

fsl/gui/guis.py

@@ -5,6 +5,7 @@
 # Author: Taylor Hanayik <hanayik@gmail.com>
 
 import os
+import random
 
 import wx
 from fsl.data import image
@@ -34,6 +35,19 @@ class BaseGui(object):
             if widget.IsTopLevel():
                 break
 
+    @staticmethod
+    def _set_rainbow(widget):
+        """
+        set the background of all panels to a random colour... I call it random unicorn mode
+        """
+        win = wx.GetTopLevelParent(widget)
+        while win.GetChildren():
+            children = win.GetChildren()
+            for win in children:
+                attr = getattr(win, 'SetBackgroundColour', None)
+                if callable(attr):
+                    win.SetBackgroundColour(wx.Colour(random.randint(0,255), random.randint(0,255), random.randint(0,255)))
+
     def layout_from(self, event):
         self._layout_from(event.GetEventObject())
 
@@ -178,6 +192,7 @@ class FlirtGui(BaseGui):
             self.model = fsltools.Flirt()
 
         self.view = fslviews.FlirtView(parent, title)
+
         self.view.mode_choice.AppendItems(self.model.flirt_type_choices)
 
         # bind events

fsl/gui/scripts/Bet_gui.py

-#!/usr/bin/env python
-
-import wx
-import sys
-from fsl.gui.guis import BetGui
-import argparse
-
-parser = argparse.ArgumentParser(description="FSL's brain extraction tool")
-parser.add_argument(
-        '-input',
-        default="",
-        type=str,
-        required=False,
-        help="an input image file"
-        )
-parser.add_argument(
-        "-output",
-        default="",
-        required=False,
-        type=str,
-        help="the output name for the brain extracted image(s)"
-        )
-parser.add_argument(
-        "-o",
-        action='store_false',
-        required=False,
-        help="generate brain surface outline overlaid onto original image"
-        )
-parser.add_argument(
-        "-m",
-        action='store_false',
-        required=False,
-        help="generate binary brain mask"
-        )
-parser.add_argument(
-        "-s",
-        action='store_false',
-        required=False,
-        help="generate approximate skull image"
-        )
-parser.add_argument(
-        "-n",
-        action='store_false',
-        required=False,
-        help="do not save segmented brain image"
-        )
-parser.add_argument(
-        "-f",
-        default=0.5,
-        type=float,
-        required=False,
-        help="do not save segmented brain image"
-        )
-
-def main():
-    args = parser.parse_args()
-
-    # get an app instance
-    app = wx.App()
-    # get our wx.Frame (this bet window will not be embedded in a panel)
-    # betview = BetView(
-    #         parent=None,
-    #         in_img=args.input,
-    #         out_img=args.output,
-    #         o_opt=args.o,
-    #         m_opt=args.m,
-    #         s_opt=args.s,
-    #         n_opt=args.n,
-    #         f_opt=args.f) # parent=None will return a wx.Frame
-    # betview.window.Show()
-    frame = wx.Frame(None, size=(800, 600))
-    sizer = wx.BoxSizer(wx.VERTICAL)
-    controller = BetGui(frame, "BET")
-    sizer.Add(controller.view, proportion=1, flag=wx.EXPAND | wx.ALL, border=5)
-    frame.SetSizer(sizer)
-    frame.Centre()
-    frame.Show()
-    app.MainLoop()
-if __name__ == "__main__":
-    sys.exit(main())

fsl/gui/scripts/bet_gui.py

+#!/usr/bin/env python
+
+import wx
+import sys
+from fsl.gui.guis import BetGui
+import argparse
+
+parser = argparse.ArgumentParser(description="FSL's brain extraction tool")
+
+def main():
+    args = parser.parse_args()
+    app = wx.App()
+    frame = wx.Frame(None, size=(800, 600))
+    sizer = wx.BoxSizer(wx.VERTICAL)
+    betgui = BetGui(frame, "BET")
+    sizer.Add(betgui.view, proportion=1, flag=wx.EXPAND | wx.ALL, border=5)
+    frame.SetSizer(sizer)
+    frame.Centre()
+    frame.Show()
+    app.MainLoop()
+if __name__ == "__main__":
+    sys.exit(main())

fsl/gui/widgets.py

@@ -6,19 +6,83 @@ import os
 import subprocess
 
 import wx
+import fsleyes
 import fsleyes.overlay as fsloverlay
 import fsleyes.displaycontext as fsldc
 import fsleyes.views.orthopanel as orthopanel
-from fsleyes.main import embed
 import fsleyes.profiles as profiles
 import fsleyes.profiles.profilemap as profilemap
-from fsleyes.frame import FSLeyesFrame
+import fsleyes.colourmaps as colourmaps
+
 from fsl.utils.platform import platform as fslplatform
 from fsl.utils import idle
 
 import fsl.data.image as fslimage
 import fsl.gui.icons as fslicons
 
+def _embed(parent=None, make_fsleyesframe=True, **kwargs):
+    """Initialise FSLeyes and create a :class:`.FSLeyesFrame`, when
+    running within another application.
+
+    .. note:: If a ``wx.App`` does not exist, one is created.
+
+    :arg parent: ``wx`` parent object
+    :arg make_fsleyesframe: bool, default is True to make a new :class:`.FSLeyesFrame`
+    :returns:    A tuple containing:
+                    - The :class:`.OverlayList`
+                    - The master :class:`.DisplayContext`
+                    - The :class:`.FSLeyesFrame` or None if make_fsleyesframe=False
+
+    All other arguments are passed to :meth:`.FSLeyesFrame.__init__`.
+    """
+
+    import fsleyes_props          as props
+    import fsleyes.gl             as fslgl
+    import fsleyes.frame          as fslframe
+    import fsleyes.overlay        as fsloverlay
+    import fsleyes.displaycontext as fsldc
+
+    app    = wx.GetApp()
+    ownapp = app is None
+    if ownapp:
+        app = FSLeyesApp()
+
+    fsleyes.initialise()
+    colourmaps.init()
+    props.initGUI()
+
+    called = [False]
+    ret    = [None]
+
+    def until():
+        return called[0]
+
+    def ready():
+        frame = None
+        fslgl.bootstrap()
+
+        overlayList = fsloverlay.OverlayList()
+        displayCtx  = fsldc.DisplayContext(overlayList)
+        if make_fsleyesframe:
+            frame       = fslframe.FSLeyesFrame(
+                parent, overlayList, displayCtx, **kwargs)
+
+        if ownapp:
+            app.SetOverlayListAndDisplayContext(overlayList, displayCtx)
+            # Keep a ref to prevent the app from being GC'd
+            if make_fsleyesframe:
+                frame._embed_app = app
+
+        called[0] = True
+        ret[0]    = (overlayList, displayCtx, frame)
+
+    fslgl.getGLContext(parent=parent, ready=ready)
+    idle.block(10, until=until)
+
+    if ret[0] is None:
+        raise RuntimeError('Failed to start FSLeyes')
+    return ret[0]
+
 def layout_from(widget):
     """
     redo layout of all widgets up the parent tree from this widget. 
@@ -285,17 +349,16 @@ class ViewProfile(profiles.Profile):
 profilemap.profiles[orthopanel.OrthoPanel].insert(0, 'minview')
 profilemap.profileHandlers[orthopanel.OrthoPanel, 'minview'] = ViewProfile
 
-def nomenu(*a):
-    pass
-FSLeyesFrame._FSLeyesFrame__makeMenuBar = nomenu
+# def nomenu(*a):
+#     pass
+# FSLeyesFrame._FSLeyesFrame__makeMenuBar = nomenu
 
 
 class OrthoView(wx.CollapsiblePane):
     def __init__(self, parent, **kwargs):
         super().__init__(parent, **kwargs)
         pane = self.GetPane()
-        self.overlayList, masterDisplayCtx, frame = embed(None)
-        frame = None
+        self.overlayList, masterDisplayCtx, _ = _embed(None, make_fsleyesframe=False)
         self.displayCtx = fsldc.DisplayContext(self.overlayList, parent=masterDisplayCtx)
 
         sizer = wx.BoxSizer(wx.VERTICAL)

requirements.txt

@@ -9,7 +9,7 @@ PyOpenGL>=3.1.0
 pyparsing==2.*
 scipy>=0.18
 wxPython>=3.0.2.0
-fslpy>=2.8.4
+fslpy>=3.0.0
 fsleyes>=0.32.3
 fsleyes-props>=1.6.7
 fsleyes-widgets>=0.8.4

setup.py

@@ -7,7 +7,7 @@ with open('requirements.txt', 'rt') as f:
 
 setup(
     name='fslgui',
-    version='0.0.0.dev7',
+    version='0.0.0.dev8',
     description='fslgui',
     url='https://git.fmrib.ox.ac.uk/fsl/fslgui',
     author='Taylor Hanayik',
@@ -27,8 +27,8 @@ setup(
     include_package_data=True,
     entry_points={
         'console_scripts' : [
-            'bet_gui        = fsl.gui.scripts.Bet_gui:main',
-            'flirt_gui        = fsl.gui.scripts.Flirt_gui:main'
+            'bet_gui        = fsl.gui.scripts.bet_gui:main',
+            'flirt_gui        = fsl.gui.scripts.flirt_gui:main'
         ]
     },
     package_data={