add bet center coords

fsl/gui/guis.py

@@ -62,12 +62,23 @@ class BetGui(BaseGui):
         self.view.options.cb_save_mask.Bind(wx.EVT_CHECKBOX, self._on_save_mask)
         self.view.options.cb_save_overlay.Bind(wx.EVT_CHECKBOX, self._on_save_overlay)
         self.view.options.cb_save_skull.Bind(wx.EVT_CHECKBOX, self._on_save_skull)
+        self.view.options.coordx.Bind(wx.EVT_SPINCTRLDOUBLE, self._on_coord_update)
+        self.view.options.coordy.Bind(wx.EVT_SPINCTRLDOUBLE, self._on_coord_update)
+        self.view.options.coordz.Bind(wx.EVT_SPINCTRLDOUBLE, self._on_coord_update)
         self.view.action_panel.play_icon.Bind(wx.EVT_LEFT_UP, self._on_run)
         self.view.action_panel.code_icon.Bind(wx.EVT_LEFT_UP, self._on_code)
         self.view.input.file_ctrl.Bind(wx.EVT_TEXT, self._on_input_edit)
         self.view.output.file_ctrl.Bind(wx.EVT_TEXT, self._on_output_edit)
         self.view.t2_input.file_ctrl.Bind(wx.EVT_TEXT, self._on_t2_input_edit)
 
+    def _on_coord_update(self, event):
+        x = self.view.options.coordx.GetValue()
+        y = self.view.options.coordy.GetValue()
+        z = self.view.options.coordz.GetValue()
+
+        self.model.center_coord = (x, y, z)
+        print(self.model.center_coord)
+
     def _on_input_edit(self, event):
         widget = event.GetEventObject()
         val = widget.GetValue()

fsl/gui/tools.py

@@ -36,6 +36,7 @@ class Bet:
                  bet_type="",
                  fval=0.5,
                  gval=0,
+                 center_coord=(),
                  discard_bet=False,
                  save_mask=False,
                  applythresh=False,
@@ -51,6 +52,7 @@ class Bet:
         self._bet_type = bet_type
         self._fval = fval
         self._gval = gval
+        self._center_coord = center_coord
         self._discard_bet = discard_bet
         self._save_mask = save_mask
         self._applythresh = applythresh
@@ -127,6 +129,15 @@ class Bet:
         assert (val >= -1) & (val <= 1), "gval must be in the range -1 .. 1"
         self._gval = val
 
+    @property
+    def center_coord(self):
+        return self._center_coord
+
+    @center_coord.setter
+    def center_coord(self, coord):
+        assert (isinstance(coord, tuple)) & (len(coord) == 3)
+        self._center_coord = coord
+
     @property
     def discard_bet(self):
         return self._discard_bet
@@ -225,6 +236,9 @@ class Bet:
 
 
     def command(self):
+        """
+        make command line string to call program
+        """
         FSLDIR = os.getenv("FSLDIR", None)
         if FSLDIR is None:
             return False
@@ -232,6 +246,7 @@ class Bet:
             return False
         if (len(self.image_t2) > 0) & (os.path.isfile(self.image_t2) is False):
             return False
+
         cmd = [
             os.path.join(FSLDIR, 'bin', 'bet'),
             self.image_in,
@@ -239,6 +254,11 @@ class Bet:
             '-f', str(self.fval),
             '-g', str(self.gval)
         ]
+
+        if self._center_coord != (0, 0, 0):
+            (x, y, z) = self._center_coord
+            cmd.extend(['-c', str(x), str(y), str(z)])
+
         for key in self._bool_argmap:
             if self._bool_argmap[key]:
                 cmd.append(key)

fsl/gui/views.py

@@ -13,6 +13,9 @@ import fsl.gui.widgets as fslwidgets
 
 class BetOptions(wx.CollapsiblePane):
     """
+    BetOptions is a collapsible pane containing widgets that control
+    bet's operation. 
+
     add the Options pane to a parent's sizer with a proportion value of 0.
     """
     def __init__(self, *args, **kwargs):
@@ -58,6 +61,25 @@ class BetOptions(wx.CollapsiblePane):
         self.gval_panel.sizer.Add(self.gval_control, 0, wx.ALL, 5)
         self.gval_panel.SetSizer(self.gval_panel.sizer)
 
+        # the bet center coordinates
+        self.coord_panel = wx.Panel(pane)
+        self.coord_panel.sizer = wx.BoxSizer(wx.HORIZONTAL)
+        self.coordx = wx.SpinCtrlDouble(self.coord_panel, min=0, max=10000, initial=0, inc=1)
+        self.coordy = wx.SpinCtrlDouble(self.coord_panel, min=0, max=10000, initial=0, inc=1)
+        self.coordz = wx.SpinCtrlDouble(self.coord_panel, min=0, max=10000, initial=0, inc=1)
+        self.label_coordstr = wx.StaticText(self.coord_panel, label="Center point: ")
+        self.labelx = wx.StaticText(self.coord_panel, label="X ")
+        self.labely = wx.StaticText(self.coord_panel, label="Y ")
+        self.labelz = wx.StaticText(self.coord_panel, label="Z ")
+        self.coord_panel.sizer.Add(self.label_coordstr, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.labelx, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.coordx, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.labely, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.coordy, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.labelz, 0, wx.ALL, 5)
+        self.coord_panel.sizer.Add(self.coordz, 0, wx.ALL, 5)
+        self.coord_panel.SetSizer(self.coord_panel.sizer)
+
         # now add all of the options widgets to the sizer
         sizer.Add(self.fval_panel, 0, wx.ALL, 0) # 0 pixel border since the fval_panel already applied a 5 pix border
         sizer.Add(self.bet_choice_panel, 0, wx.ALL, 0)
@@ -67,13 +89,17 @@ class BetOptions(wx.CollapsiblePane):
         sizer.Add(self.cb_save_skull, 0, wx.ALL, 5)
         sizer.Add(self.cb_save_overlay, 0, wx.ALL, 5)
         sizer.Add(self.cb_verbose, 0, wx.ALL, 5)
-        sizer.Add(self.gval_panel, 0,wx.ALL, 0)
+        sizer.Add(self.gval_panel, 0, wx.ALL, 0)
+        sizer.Add(self.coord_panel, 0, wx.ALL, 0)
 
 
         # now layout the widgets so they can be sized appropriately (automatically done by wx)
         pane.SetSizer(sizer)
 
 class BetView(wx.Panel):
+    """
+    Bet view defines the graphical layout of widgets for using BET
+    """
     def __init__(self, parent, title="BET", **kwargs):
         super().__init__(parent, **kwargs)
         self.parent     = parent
@@ -113,5 +139,15 @@ class BetView(wx.Panel):
         self.SetSizer(sizer)
 
 
-class FslStartup():
-    pass
\ No newline at end of file
+class FlirtView():
+    """
+    FlirtView defines the graphical layout of widgets used in Flirt
+    """
+    
+
+class FslView():
+    """
+    FslView is the main FSL start window.
+    """
+    
+

fsl/gui/widgets.py

+"""
+the widges module provides common widgets that are intended
+to be embedded within other FSL guis.  
+"""
 import os
+
 import wx
 import fsleyes.overlay as fsloverlay
 import fsleyes.displaycontext as fsldc
 import fsleyes.views.orthopanel as orthopanel
-import fsl.data.image as fslimage
 from fsleyes.main import embed
 import fsleyes.profiles as profiles
 import fsleyes.profiles.profilemap as profilemap
 from fsleyes.frame import FSLeyesFrame
+
+import fsl.data.image as fslimage
 import fsl.gui.icons as fslicons
 
 def layout_from(widget):