fine tune bet and start flirt gui

fsl/gui/guis.py

@@ -165,3 +165,31 @@ class BetGui(BaseGui):
         self._on_code(None)
         self.model.run(self._load_result)
 
+
+class FlirtGui(BaseGui):
+    """
+    The FlirtGui is the controller for the FlirtView that
+    can interact with the flirt model
+    """
+    def __init__(self, parent, title="FLIRT", model=None):
+        super().__init__()
+
+        if model is None:
+            self.model = fsltools.Flirt()
+
+        self.view = fslviews.FlirtView(parent, title)
+        self.view.mode_choice.AppendItems(self.model.flirt_type_choices)
+
+        # bind events
+        self.view.mode_choice.Bind(wx.EVT_CHOICE, self._on_mode_choice)
+
+    def _on_mode_choice(self, event):
+        widget = event.GetEventObject()
+        idx = widget.GetSelection()
+        choice_str = widget.GetString(idx)
+        if 'lowres' in choice_str:
+            self.view.input_lowres.Show()
+            self._layout_from(self.view.input_lowres)
+        else:
+            self.view.input_lowres.Hide()
+            self._layout_from(self.view.input_lowres)
\ No newline at end of file

fsl/gui/scripts/Flirt_gui

+#!/usr/bin/env pythonw
+
+import wx
+import sys
+from fsl.gui.guis import FlirtGui
+import argparse
+
+parser = argparse.ArgumentParser(description="FSL's FLIRT")
+parser.add_argument(
+        '-input',
+        default="",
+        type=str,
+        required=False,
+        help="an input image file")
+
+def main():
+    args = parser.parse_args()
+
+    # get an app instance
+    app = wx.App()
+    frame = wx.Frame(None, size=(800, 600))
+    sizer = wx.BoxSizer(wx.VERTICAL)
+    flirt_gui = FlirtGui(frame, "FLIRT")
+    sizer.Add(flirt_gui.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())
\ No newline at end of file

fsl/gui/tools.py

@@ -13,7 +13,7 @@ from fsl.utils import idle
 
 
 
-class Bet:
+class Bet(object):
     """
     A BetModel contains the data and methods necessary to setup and run FSL's bet tool.
     The BetModel can be queried and properties can be set via a controller of a GUI view object
@@ -36,7 +36,7 @@ class Bet:
                  bet_type="",
                  fval=0.5,
                  gval=0,
-                 center_coord=(),
+                 center_coord=(0, 0, 0),
                  discard_bet=False,
                  save_mask=False,
                  applythresh=False,
@@ -270,3 +270,12 @@ class Bet:
                 cmd.append(self.bet_type)
         print(" ".join(cmd))
         return cmd
+
+
+class Flirt(object):
+    flirt_type_choices = [
+        "highres to standard",
+        "lowres to highres to standard"
+    ]
+    def __init__(self, in_highres=""):
+        pass
\ No newline at end of file

fsl/gui/views.py

@@ -139,15 +139,53 @@ class BetView(wx.Panel):
         self.SetSizer(sizer)
 
 
-class FlirtView():
+class FlirtView(wx.Panel):
     """
     FlirtView defines the graphical layout of widgets used in Flirt
     """
+    def __init__(self, parent, title="FLIRT", **kwargs):
+        super().__init__(parent, **kwargs)
+        sizer = wx.BoxSizer(wx.VERTICAL)
+
+        # title panel
+        #------------
+        self.title_panel = fslwidgets.Title(self, title)
+        sizer.Add(self.title_panel, proportion=0, flag=wx.ALIGN_CENTER | wx.ALL, border=5)
+
+
+        # mode selection panel
+        #---------------------
+        mode_panel = wx.Panel(self)
+        mode_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        mode_st = wx.StaticText(mode_panel, label="Mode")
+        # make mode_choice an attribute to be updated by the controller
+        self.mode_choice = wx.Choice(mode_panel, choices=[])
+        mode_sizer.Add(mode_st, proportion=0, flag=wx.ALL, border=5)
+        mode_sizer.Add(self.mode_choice, proportion=0, flag=wx.ALL, border=5)
+        mode_panel.SetSizer(mode_sizer)
+        sizer.Add(mode_panel, proportion=0, flag=wx.ALL, border=5)
+
+        # low res input panel (hidden when mode is highres to standard)
+        self.input_lowres = fslwidgets.Input(self).set_label("Lowres image*")
+        sizer.Add(self.input_lowres, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
+        self.input_lowres.Hide()
+        
+        # high res input panel
+        self.input_highres = fslwidgets.Input(self).set_label("Highres image*")
+        sizer.Add(self.input_highres, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
+
+        # reference image picker panel
+        self.input_reference = fslwidgets.ReferencePicker(self).set_label("Reference image*")
+        sizer.Add(self.input_reference, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
+
+        self.SetSizer(sizer)
+
     
 
 class FslView():
     """
-    FslView is the main FSL start window.
+    FslView is the main FSL start window. not to be 
+    confused with the deprecated image viewer fslview (RIP)
     """
     
 

fsl/gui/widgets.py

@@ -3,6 +3,7 @@ the widges module provides common widgets that are intended
 to be embedded within other FSL guis.  
 """
 import os
+import subprocess
 
 import wx
 import fsleyes.overlay as fsloverlay
@@ -12,6 +13,8 @@ from fsleyes.main import embed
 import fsleyes.profiles as profiles
 import fsleyes.profiles.profilemap as profilemap
 from fsleyes.frame import FSLeyesFrame
+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
@@ -27,15 +30,31 @@ def layout_from(widget):
         if widget.IsTopLevel():
             break
 
+class FileDropTextCtrl(wx.FileDropTarget):
+    """
+    Drop target specifically for wx.TextCtrl widgets.
+    It's specific because it expects window to have a SetValue method
+    """
+    def __init__(self, window):
+        wx.FileDropTarget.__init__(self)
+        self.window = window
+
+    def OnDropFiles(self, x, y, filenames):
+        # only use the first file if multiple are dropped at once
+        self.window.SetValue(filenames[0])
+        return True
+
 class Input(wx.Panel):
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
+    def __init__(self, parent, **kwargs):
+        wx.Panel.__init__(self, parent)
         self.file_path = ""
         #sizer = wx.StaticBoxSizer(wx.HORIZONTAL, self, "Input image*")
         self.box = wx.StaticBox(self, label="")
         sizer = wx.StaticBoxSizer(self.box)
         self.button = wx.Button(self.box, label="Choose")
         self.file_ctrl = wx.TextCtrl(self.box, value="")
+        drop_target = FileDropTextCtrl(self.file_ctrl)
+        self.file_ctrl.SetDropTarget(drop_target)
         sizer.Add(self.file_ctrl, 1, wx.EXPAND | wx.ALL, 5)
         sizer.Add(self.button, 0, wx.ALL, 5)
         self.SetSizer(sizer)
@@ -61,6 +80,75 @@ class Input(wx.Panel):
             self.file_path = os.path.abspath(fd.GetPath())
             self.set_text(self.file_path)
 
+class ReferencePicker(wx.Panel):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.file_path = ""
+        #sizer = wx.StaticBoxSizer(wx.HORIZONTAL, self, "Input image*")
+        self.box = wx.StaticBox(self, label="Reference image")
+        sizer = wx.StaticBoxSizer(self.box, orient=wx.VERTICAL)
+        input_panel = wx.Panel(self.box)
+        input_panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        self.choose_button = wx.Button(input_panel, label="Choose")
+        self.file_ctrl = wx.TextCtrl(input_panel, value="")
+        input_panel_sizer.Add(self.file_ctrl, 1, wx.EXPAND | wx.ALL, 5)
+        input_panel_sizer.Add(self.choose_button, 0, wx.ALL, 5)
+        input_panel.SetSizer(input_panel_sizer)
+
+        button_panel = wx.Panel(self.box)
+        button_panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        self.btn_1mm_brain = wx.Button(button_panel, label="standard_1mm_brain")
+        self.btn_2mm_brain = wx.Button(button_panel, label="standard_2mm_brain")
+        button_panel_sizer.Add(self.btn_1mm_brain, proportion=0, flag=wx.ALL, border=5)
+        button_panel_sizer.Add(self.btn_2mm_brain, proportion=0, flag=wx.ALL, border=5)
+        button_panel.SetSizer(button_panel_sizer)
+
+
+        sizer.Add(input_panel, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
+        sizer.Add(button_panel, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
+        self.SetSizer(sizer)
+
+        self.choose_button.Bind(wx.EVT_LEFT_UP, self._on_choose)
+        self.btn_1mm_brain.Bind(wx.EVT_LEFT_UP, self._on_1mm_brain)
+        self.btn_2mm_brain.Bind(wx.EVT_LEFT_UP, self._on_2mm_brain)
+
+    def set_label(self, text):
+        self.box.SetLabel(text)
+        layout_from(self.box)
+        return self
+
+    def set_text(self, text):
+        self.file_ctrl.SetValue(text)
+        return self
+
+    def get_path(self):
+        return self.file_ctrl.GetValue()
+
+    def _on_choose(self, event):
+        with wx.FileDialog(self, "Choose input file", style=wx.FD_OPEN) as fd:
+            if fd.ShowModal() == wx.ID_CANCEL:
+                return
+            self.file_path = os.path.abspath(fd.GetPath())
+            self.set_text(self.file_path)
+
+    def _on_1mm_brain(self, event):
+        self.file_path = os.path.join(
+            fslplatform.fsldir,
+            "data",
+            "standard",
+            "MNI152_T1_1mm_brain.nii.gz"
+        )
+        self.set_text(self.file_path)
+
+    def _on_2mm_brain(self, event):
+        self.file_path = os.path.join(
+            fslplatform.fsldir,
+            "data",
+            "standard",
+            "MNI152_T1_2mm_brain.nii.gz"
+        )
+        self.set_text(self.file_path)
+
 
 class Output(wx.Panel):
     def __init__(self, *args, **kwargs):
@@ -218,9 +306,32 @@ class OrthoView(wx.CollapsiblePane):
                 None)
         self.op.SetMinSize((-1, 300))
         self.op.Show()
-        sizer.Add(self.op, 1, wx.EXPAND | wx.ALL, 5)
+
+        self.btn_fsleyes = wx.Button(pane, label="Open in FSLeyes")
+        sizer.Add(self.btn_fsleyes, proportion=0, flag=wx.ALL, border=5)
+        sizer.Add(self.op, proportion=1, flag=wx.EXPAND | wx.ALL, border=5)
         pane.SetSizer(sizer)
 
+        # bind events
+        self.btn_fsleyes.Bind(wx.EVT_BUTTON, self.launch_fsleyes)
+    
+    def _run_fsleyes(self):
+        imgs = [img.dataSource for img in self.overlayList]
+        # print([img.dataSource for img in self.overlayList])
+        cmd = [
+            os.path.join(fslplatform.fsldir, 'bin', 'fsleyes'),
+            " ".join(imgs)
+        ]
+        subprocess.run(
+            " ".join(cmd),
+            shell=True, 
+            check=True
+        )
+
+
+    def launch_fsleyes(self, event):
+        thread_id = idle.run(self._run_fsleyes)
+
     def reset(self):
         self.overlayList.clear()