diff --git a/fsl/fsleyes/actions/runscript.py b/fsl/fsleyes/actions/runscript.py
index 17e37bca9bf6a20dc61223f66d1d9a5b15f4ab05..18637312fd9a95a66d8e4dd7ede28997a879f65a 100644
--- a/fsl/fsleyes/actions/runscript.py
+++ b/fsl/fsleyes/actions/runscript.py
@@ -6,6 +6,15 @@
#
"""This module provides the :class:`RunScriptAction` class, which allows
the user to run a custom Python script.
+
+The following functions are used by the :class:`RunScriptAction`, and are
+available for other purposes:
+
+ .. autosummary::
+ :nosignatures:
+
+ runScript
+ fsleyesScriptEnvironment
"""
@@ -45,35 +54,47 @@ class RunScriptAction(action.Action):
self.__displayCtx = displayCtx
- def __doAction(self):
- """Called when this :class:`.Action` is invoked. Prompts the user to
- select a script file, then compiles and runs the script.
+ def __doAction(self, script=None):
+ """Called when this :class:`.Action` is invoked. If the ``script``
+ argument is ``None``, the user is prompted to select a script file.
+ The script is then compiled and executed.
"""
import wx
- lastDir = fslsettings.read('runScriptLastDir')
+ if script is None:
- if lastDir is None:
- lastDir = os.getcwd()
+ lastDir = fslsettings.read('runScriptLastDir')
- msg = strings.messages[self, 'runScript']
+ if lastDir is None:
+ lastDir = os.getcwd()
- # Ask the user what script
- # they want to run
- dlg = wx.FileDialog(self.__frame,
- message=msg,
- defaultDir=lastDir,
- wildcard='*.py',
- style=wx.FD_OPEN)
+ msg = strings.messages[self, 'runScript']
- if dlg.ShowModal() != wx.ID_OK:
- return
+ # Ask the user what script
+ # they want to run
+ dlg = wx.FileDialog(self.__frame,
+ message=msg,
+ defaultDir=lastDir,
+ wildcard='*.py',
+ style=wx.FD_OPEN)
- script = dlg.GetPath()
-
+ if dlg.ShowModal() != wx.ID_OK:
+ return
+
+ script = dlg.GetPath()
+
+ # Save the script directory for the
+ # next time the user is prompted
+ fslsettings.write('runScriptLastDir', op.dirname(script))
+
+ # Run the script, show an
+ # error if it crashes
try:
- self.__runScript(script)
+ runScript(self.__frame,
+ self.__overlayList,
+ self.__displayCtx,
+ script)
except Exception as e:
log.warning('Script ({}) could not be executed: {}'.format(
@@ -91,49 +112,74 @@ class RunScriptAction(action.Action):
return
- # Save the script directory
- # for the next time the user
- # is prompted
- fslsettings.write('runScriptLastDir', op.dirname(script))
-
- def __runScript(self, script):
- """Compiles and executes the given file, assumed to be a Python script.
- An ``Error`` is raised if the script cannot be compiled or executed.
- """
+def runScript(frame, overlayList, displayCtx, script):
+ """Compiles and executes the given file, assumed to be a Python script.
+ An ``Error`` is raised if the script cannot be compiled or executed.
+ """
- # Set up the script environment. It's
- # quite difficult to truly sand-box an
- # eval'ed piece of code, but setting
- # __builtins__ to None will deter simple
- # attack attempts.
- _globals = {
- '__builtins__' : None
- }
-
- _locals = {
- 'overlayList' : self.__overlayList,
- 'displayCtx' : self.__displayCtx,
- 'frame' : self.__frame,
- 'viewPanels' : self.__frame.getViewPanels()
- }
-
- # We want scripts to be Python3-like
- flags = (futures.print_function .compiler_flag |
- futures.absolute_import .compiler_flag |
- futures.division .compiler_flag |
- futures.unicode_literals.compiler_flag)
-
- # Compile the script
- with open(script, 'rt') as f:
- log.debug('Compiling {}...'.format(script))
- code = f.read()
- code = compile(code,
- script,
- mode='exec',
- flags=flags,
- dont_inherit=True)
-
- # Run the script
- log.debug('Running {}...'.format(script))
- eval(code, _globals, _locals)
+ # We want scripts to be Python3-like
+ flags = (futures.print_function .compiler_flag |
+ futures.absolute_import .compiler_flag |
+ futures.division .compiler_flag |
+ futures.unicode_literals.compiler_flag)
+
+ # Compile the script
+ with open(script, 'rt') as f:
+ log.debug('Compiling {}...'.format(script))
+ code = f.read()
+ code = compile(code,
+ script,
+ mode='exec',
+ flags=flags,
+ dont_inherit=True)
+
+ _globals, _locals = fsleyesScriptEnvironment(frame,
+ overlayList,
+ displayCtx)
+
+ # Run the script
+ log.debug('Running {}...'.format(script))
+ eval(code, _globals, _locals)
+
+
+def fsleyesScriptEnvironment(frame, overlayList, displayCtx):
+ """Creates and returns two dictionaries, to be used as the ``globals``
+ and ``locals`` dictionaries when executing a custom FSLeyes python
+ script.
+ """
+
+ # Set up the script environment. It's
+ # quite difficult to truly sand-box an
+ # eval'ed piece of code, but restricting
+ # the things contained in__builtins__
+ # will deter simple attack attempts.
+ _globals = {
+ '__builtins__' : {
+ 'True' : True,
+ 'False' : False
+ },
+ }
+
+ import fsl.fsleyes.views as views
+ import fsl.fsleyes.controls as controls
+ import fsl.data.image as image
+ import fsl.data.featimage as featimage
+ import fsl.data.melodicimage as melimage
+ import fsl.data.tensorimage as tensorimage
+ import fsl.data.model as model
+
+ _locals = {
+ 'Image' : image.Image,
+ 'FEATImage' : featimage.FEATImage,
+ 'MelodicImage' : melimage.MelodicImage,
+ 'TensorImage' : tensorimage.TensorImage,
+ 'Model' : model.Model,
+ 'views' : views,
+ 'controls' : controls,
+ 'overlayList' : overlayList,
+ 'displayCtx' : displayCtx,
+ 'frame' : frame,
+ }
+
+ return _globals, _locals
diff --git a/fsl/fsleyes/frame.py b/fsl/fsleyes/frame.py
index d71d3850d2af1acf61ff00072cba6cc9ef6e95db..c4921a49995cb51d3bc3c42802c06449cbce0a56 100644
--- a/fsl/fsleyes/frame.py
+++ b/fsl/fsleyes/frame.py
@@ -404,9 +404,13 @@ class FSLEyesFrame(wx.Frame):
self.__makePerspectiveMenu()
- def runScript(self):
+ def runScript(self, script=None):
"""Runs a custom python script, via a :class:`.RunScriptAction`. """
- actions.RunScriptAction(self.__overlayList, self.__displayCtx, self)()
+
+ rsa = actions.RunScriptAction(self.__overlayList,
+ self.__displayCtx,
+ self)
+ rsa(script)
def __addViewPanelMenu(self, panel, title):
diff --git a/fsl/fsleyes/views/shellpanel.py b/fsl/fsleyes/views/shellpanel.py
index fc145d9fe70016b7f84cc92161174d81783e3976..36152f3e0161816e5b27a43e32ee6dd7474c3419 100644
--- a/fsl/fsleyes/views/shellpanel.py
+++ b/fsl/fsleyes/views/shellpanel.py
@@ -15,6 +15,8 @@ import wx.py.shell as wxshell
from . import viewpanel
+import fsl.fsleyes.actions.runscript as runscript
+
class ShellPanel(viewpanel.ViewPanel):
"""A ``ShellPanel`` is a :class:`.ViewPanel` which contains an
@@ -42,22 +44,19 @@ class ShellPanel(viewpanel.ViewPanel):
"""
viewpanel.ViewPanel.__init__(self, parent, overlayList, displayCtx)
- lcls = {
- 'displayCtx' : displayCtx,
- 'overlayList' : overlayList,
- 'frame' : frame,
- 'viewPanel' : parent,
- }
+ _globals, _locals = runscript.fsleyesScriptEnvironment(frame,
+ overlayList,
+ displayCtx)
+
shell = wxshell.Shell(
self,
introText=' FSLEyes python shell\n\n'
- 'Available variables are:\n'
+ 'Available FSLeyes variables are:\n'
' - overlayList\n'
' - displayCtx\n'
- ' - frame\n'
- ' - viewPanel\n\n',
- locals=lcls,
+ ' - frame\n',
+ locals=_locals,
showInterpIntro=False)
# TODO set up environment so that users can
@@ -66,14 +65,12 @@ class ShellPanel(viewpanel.ViewPanel):
#
# - Load overlays from a URL
#
- # - make plots - already possible with pylab, but make
- # sure it works properly (i.e. doesn't clobber the shell)
+ # - make plots
#
# - run scripts (add a 'load/run' button)
#
# - open/close view panels, and manipulate existing view panels
#
- shell.push('from pylab import *\n')
font = shell.GetFont()
diff --git a/fsl/tools/fsleyes.py b/fsl/tools/fsleyes.py
index aedafad4b627b68ec61667bb2cc39ff0737659fe..1a119166adff2a9dae99bba369707af984d23992 100644
--- a/fsl/tools/fsleyes.py
+++ b/fsl/tools/fsleyes.py
@@ -66,6 +66,10 @@ def parseArgs(argv):
add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter)
+ parser.add_argument('-r', '--runscript',
+ metavar='SCRIPTFILE',
+ help='Run custom FSLeyes script')
+
# TODO Dynamically generate perspective list
# in description. To do this, you will need
# to make fsl.utils.settings work without a
@@ -78,7 +82,10 @@ def parseArgs(argv):
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.
+ If no '--scene' is specified, the previous layout is restored, unless
+ a script is provided via the '--runscript' argument, in which case
+ it is assumed that the script sets up the scene, so the previous
+ layout is not restored.
""")
# Options for configuring the scene are
@@ -86,7 +93,8 @@ def parseArgs(argv):
return fsleyes_parseargs.parseArgs(parser,
argv,
name,
- description)
+ description,
+ fileOpts=['r', 'runscript'])
def context(args, splash):
@@ -205,6 +213,7 @@ def interface(parent, args, ctx):
overlayList, displayCtx, splashFrame = ctx
+ # Set up the frame scene (a.k.a. layout, perspective)
# The scene argument can be:
#
# - 'lightbox' or 'ortho', specifying a single view
@@ -212,13 +221,16 @@ def interface(parent, args, ctx):
#
# - The name of a saved (or built-in) perspective
#
- # - None, in which case the previous layout is restored
- scene = args.scene
+ # - None, in which case the previous layout is restored,
+ # unless a custom script has been provided.
+ script = args.runscript
+ scene = args.scene
- # If a scene or perspective has not been
- # specified, the default behaviour is to
- # restore the previous frame layout.
- restore = scene is None
+ # If a scene/perspective or custom script
+ # has not been specified, the default
+ # behaviour is to restore the previous
+ # frame layout.
+ restore = (scene is None) and (script is None)
status.update('Creating FSLeyes interface...')
@@ -253,17 +265,15 @@ def interface(parent, args, ctx):
else:
wx.CallLater(250, splashFrame.Close)
+ status.update('Setting up scene...')
+
# 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
- # (i.e. either OrthoPanel or LightBoxPanel)
+ # Apply any view-panel specific arguments
viewPanels = frame.getViewPanels()
-
- status.update('Setting up scene...')
-
for viewPanel in viewPanels:
if not isinstance(viewPanel, views.CanvasPanel):
@@ -286,6 +296,15 @@ def interface(parent, args, ctx):
if isinstance(viewPanel, views.OrthoPanel):
async.idle(centre)
+
+ # If a script has been specified, we run
+ # the script. This has to be done on the
+ # idle loop, because overlays specified
+ # on the command line are loaded on the
+ # idle loop, and the script may assume
+ # that they have already been loaded.
+ if script is not None:
+ async.idle(frame.runScript, script)
return frame