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Commit 5d7bfe4d authored by Paul McCarthy's avatar Paul McCarthy
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A custom FSLeyes script can now be specified on the command line. The 

ShellPanel uses the same environment as used by the RunScriptAction
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fsl/fsleyes/actions/runscript.py
+ 109
− 63
View file @ 5d7bfe4d
......@@ -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
fsl/fsleyes/frame.py
+ 6
− 2
View file @ 5d7bfe4d
......@@ -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):
......
fsl/fsleyes/views/shellpanel.py
+ 10
− 13
View file @ 5d7bfe4d
......@@ -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()
......
fsl/tools/fsleyes.py
+ 32
− 13
View file @ 5d7bfe4d
......@@ -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
......
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