diff --git a/fsl.py b/fsl.py
deleted file mode 100755
index e3685c2859af6676b81b7d64f8e439a5f4b9ebe6..0000000000000000000000000000000000000000
--- a/fsl.py
+++ /dev/null
@@ -1,283 +0,0 @@
-#!/usr/bin/env python
-#
-# fsl.py - Front end to FSL tools.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-
-import os
-import sys
-import logging
-import argparse
-
-# There's a bug in OpenGL.GL.shaders (which has been fixed in
-# the latest version) - it calls logging.basicConfig(), and
-# thus screws up our own logging. We overcome this by configuring
-# the root logger before OpenGL.GL.shaders is imported (which
-# occurs when fsl.fslview.gl.slicecanvas.SliceCanvas is imported).
-logging.basicConfig(
- format='%(levelname)8.8s '
- '%(filename)20.20s '
- '%(lineno)4d: '
- '%(funcName)-15.15s - '
- '%(message)s')
-log = logging.getLogger('fsl')
-
-import fsl.tools as tools
-
-def loadAllFSLTools():
- """
- Looks in the fsl.tools package, loads a description for
- every FSL tool present, and returns all descriptions in
- a {toolName->toolObj} dictionary. See loadFSLTool.
- """
-
- allTools = {}
-
- for moduleName in dir(tools):
-
- module = getattr(tools, moduleName)
-
- try: fsltool = loadFSLTool(moduleName, module)
- except TypeError: continue
-
- allTools[moduleName] = fsltool
-
- return allTools
-
-
-
-def loadFSLTool(moduleName, module):
- """
- Inspects the given module to see if it looks like a valid
- FSL tool. If it is not, a TypeError is raised. If it is,
- a container object is created and returned, containing
- all of the elements of the tool.
- """
-
- # Each FSL tool module may specify several things
- toolName = getattr(module, 'FSL_TOOLNAME', None)
- helpPage = getattr(module, 'FSL_HELPPAGE', 'index')
- parseArgs = getattr(module, 'FSL_PARSEARGS', None)
- context = getattr(module, 'FSL_CONTEXT', None)
- interface = getattr(module, 'FSL_INTERFACE', None)
- execute = getattr(module, 'FSL_EXECUTE', None)
- actions = getattr(module, 'FSL_ACTIONS', [])
-
- # But at the very least, must specify a name, and
- # either a function which will create an interface,
- # or a function which can be called to do some work
- if not all((toolName, any((interface, execute)))):
- raise TypeError('"{}" does not appear to be a valid FSL tool'.format(
- moduleName))
-
- # The tool must either provide an interface,
- # or do some non-interactive work.
- if interface and execute:
- raise TypeError('"{}" does not appear to be a valid FSL tool'.format(
- moduleName))
-
- class FSLTool(object):
- pass
-
- fsltool = FSLTool()
-
- fsltool.module = module
- fsltool.moduleName = moduleName
- fsltool.toolName = toolName
- fsltool.helpPage = helpPage
- fsltool.parseArgs = parseArgs
- fsltool.context = context
- fsltool.interface = interface
- fsltool.execute = execute
- fsltool.actions = actions
-
- return fsltool
-
-
-def parseArgs(argv, allTools):
- """
- Creates a command line ArgumentParser which will process general
- arguments for fsl.py (this script) and, arguments for all FSL
- tools which have defined their own command line arguments (see
- loadFSLTool). Returns an object containing values for all of the
- arguments that were passed in.
- """
-
- epilog = 'Type fsl.py help <tool> for program-specific help. ' \
- 'Available programs:\n {}'.format('\n '.join(allTools.keys()))
-
- parser = argparse.ArgumentParser(
- description='Run a FSL program',
- epilog=epilog,
- formatter_class=argparse.RawDescriptionHelpFormatter)
-
- parser.add_argument(
- '-v', '--verbose', action='count',
- help='Verbose output (can be used up to 3 times)')
- parser.add_argument(
- '-w', '--wxinspect', action='store_true',
- help='Run wx inspection tool')
- parser.add_argument('tool', help='FSL program to run')
-
- # find the index of the first positional argument
- try:
- firstPos = map(lambda a: not a.startswith('-'), argv).index(True)
- except ValueError:
- firstPos = len(argv)
-
- # Separate the top level arguments
- # from the tool arguments, and parse
- # the top level args
- fslArgv = argv[:firstPos + 1]
- toolArgv = argv[ firstPos + 1:]
- namespace = parser.parse_args(fslArgv)
-
- # if the specified tool is 'help', it should be followed by
- # one more argument, the name of the tool to print help for
- if namespace.tool == 'help':
-
- # no tool name supplied
- if len(toolArgv) == 0:
- parser.print_help()
- sys.exit(1)
-
- # unknown tool name supplied
- if toolArgv[0] not in allTools:
- print '\nUnknown FSL tool: {}\n'.format(namespace.tool)
- parser.print_help()
- sys.exit(1)
-
- fslTool = allTools[toolArgv[0]]
-
- # no tool specific argument parser
- if fslTool.parseArgs is None:
- print 'No help for {}'.format(toolArgv[0])
-
- # Otherwise, get help from the tool. We assume that
- # all the argument parser for every tool will interpret
- # '-h' as '--help', and will print some help
- else:
- fslTool.parseArgs(['-h'])
- sys.exit(0)
-
- # Unknown tool name supplied
- elif namespace.tool not in allTools:
- print '\nUnknown FSL tool: {}\n'.format(namespace.tool)
- parser.print_help()
- sys.exit(1)
-
- # otherwise, give the remaining arguments to the tool parser
- fslTool = allTools[namespace.tool]
-
- if fslTool.parseArgs is not None: toolArgs = fslTool.parseArgs(toolArgv)
- else: toolArgs = None
-
- return fslTool, namespace, toolArgs
-
-
-def fslDirWarning(frame, toolName, fslEnvActive):
- """
- If fslEnvActive is False, displays a warning.
- """
-
- if fslEnvActive: return
-
- msg = 'The FSLDIR environment variable is not set - '\
- '{} may not behave correctly.'.format(toolName)
-
- if frame is not None:
- import wx
- wx.MessageDialog(
- frame,
- message=msg,
- style=wx.OK | wx.ICON_EXCLAMATION).ShowModal()
- else:
- log.warn(msg)
-
-
-def buildGUI(args, fslTool, toolCtx, fslEnvActive):
- """
- """
-
- import wx
- import fsl.utils.webpage as webpage
-
- frame = fslTool.interface(None, args, ctx)
-
- menuBar = frame.GetMenuBar()
-
- if menuBar is None:
- menuBar = wx.MenuBar()
- frame.SetMenuBar(menuBar)
-
- fslMenu = wx.Menu()
- menuBar.Insert(0, fslMenu, 'FSL')
-
- actions = []
-
- actions.append((
- wx.ID_HELP,
- '{} Help'.format(fslTool.toolName),
- lambda *ev: webpage.openFSLHelp(fslTool.helpPage)))
-
- for (name, func) in fslTool.actions:
- actions.append((wx.ID_ANY, name, lambda ev, f=func: f(frame, ctx)))
-
- actions.append((
- wx.ID_EXIT,
- 'Exit',
- lambda *ev: frame.Close()))
-
- for wxId, name, func in actions:
- menuItem = fslMenu.Append(wxId, name)
- frame.Bind(wx.EVT_MENU, func, menuItem)
-
- return frame
-
-
-if __name__ == '__main__':
-
- fsldir = os.environ.get('FSLDIR', None)
- fslEnvActive = fsldir is not None
-
- allTools = loadAllFSLTools()
- fslTool, args, toolArgs = parseArgs(sys.argv[1:], allTools)
-
- if args.verbose == 1:
- log.setLevel(logging.DEBUG)
-
- # make some noisy things quiet
- logging.getLogger('fsl.fslview.gl') .setLevel(logging.WARNING)
- logging.getLogger('fsl.fslview.views').setLevel(logging.WARNING)
- logging.getLogger('props') .setLevel(logging.WARNING)
- logging.getLogger('pwidgets') .setLevel(logging.WARNING)
- elif args.verbose == 2:
- log.setLevel(logging.DEBUG)
- logging.getLogger('props') .setLevel(logging.WARNING)
- logging.getLogger('pwidgets').setLevel(logging.WARNING)
- elif args.verbose == 3:
- log.setLevel(logging.DEBUG)
- logging.getLogger('props') .setLevel(logging.DEBUG)
- logging.getLogger('pwidgets').setLevel(logging.DEBUG)
-
- if fslTool.context is not None: ctx = fslTool.context(toolArgs)
- else: ctx = None
-
- if fslTool.interface is not None:
- import wx
- app = wx.App()
- frame = buildGUI(toolArgs, fslTool, ctx, fslEnvActive)
- frame.Show()
-
- wx.CallLater(1, fslDirWarning, frame, fslTool.toolName, fslEnvActive)
-
- if args.wxinspect:
- import wx.lib.inspection
- wx.lib.inspection.InspectionTool().Show()
-
- app.MainLoop()
-
- elif fslTool.execute is not None:
- fslDirWarning( None, fslTool.toolName, fslEnvActive)
- fslTool.execute(toolArgs, ctx)
diff --git a/fsl/__init__.py b/fsl/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..c4d539840456fc9791b51e0b03514b0b792e73d6 100644
--- a/fsl/__init__.py
+++ b/fsl/__init__.py
@@ -0,0 +1,288 @@
+#!/usr/bin/env python
+#
+# __init__.py - Front end to fslpy. The entry point is main(), defined
+# at the bottom.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import logging
+log = logging.getLogger(__name__)
+
+import os
+import sys
+import logging
+import argparse
+
+# There's a bug in OpenGL.GL.shaders (which has been fixed in
+# the latest version) - it calls logging.basicConfig(), and
+# thus screws up our own logging. We overcome this by configuring
+# the root logger before OpenGL.GL.shaders is imported (which
+# occurs when fsl.fslview.gl.slicecanvas.SliceCanvas is imported).
+logging.basicConfig(
+ format='%(levelname)8.8s '
+ '%(filename)20.20s '
+ '%(lineno)4d: '
+ '%(funcName)-15.15s - '
+ '%(message)s')
+log = logging.getLogger('fsl')
+
+import fsl.tools as tools
+
+def loadAllFSLTools():
+ """
+ Looks in the fsl.tools package, loads a description for
+ every FSL tool present, and returns all descriptions in
+ a {toolName->toolObj} dictionary. See loadFSLTool.
+ """
+
+ allTools = {}
+
+ for moduleName in dir(tools):
+
+ module = getattr(tools, moduleName)
+
+ try: fsltool = loadFSLTool(moduleName, module)
+ except TypeError: continue
+
+ allTools[moduleName] = fsltool
+
+ return allTools
+
+
+
+def loadFSLTool(moduleName, module):
+ """
+ Inspects the given module to see if it looks like a valid
+ FSL tool. If it is not, a TypeError is raised. If it is,
+ a container object is created and returned, containing
+ all of the elements of the tool.
+ """
+
+ # Each FSL tool module may specify several things
+ toolName = getattr(module, 'FSL_TOOLNAME', None)
+ helpPage = getattr(module, 'FSL_HELPPAGE', 'index')
+ parseArgs = getattr(module, 'FSL_PARSEARGS', None)
+ context = getattr(module, 'FSL_CONTEXT', None)
+ interface = getattr(module, 'FSL_INTERFACE', None)
+ execute = getattr(module, 'FSL_EXECUTE', None)
+ actions = getattr(module, 'FSL_ACTIONS', [])
+
+ # But at the very least, must specify a name, and
+ # either a function which will create an interface,
+ # or a function which can be called to do some work
+ if not all((toolName, any((interface, execute)))):
+ raise TypeError('"{}" does not appear to be a valid FSL tool'.format(
+ moduleName))
+
+ # The tool must either provide an interface,
+ # or do some non-interactive work.
+ if interface and execute:
+ raise TypeError('"{}" does not appear to be a valid FSL tool'.format(
+ moduleName))
+
+ class FSLTool(object):
+ pass
+
+ fsltool = FSLTool()
+
+ fsltool.module = module
+ fsltool.moduleName = moduleName
+ fsltool.toolName = toolName
+ fsltool.helpPage = helpPage
+ fsltool.parseArgs = parseArgs
+ fsltool.context = context
+ fsltool.interface = interface
+ fsltool.execute = execute
+ fsltool.actions = actions
+
+ return fsltool
+
+
+def parseArgs(argv, allTools):
+ """
+ Creates a command line ArgumentParser which will process general
+ arguments for fsl.py (this script) and, arguments for all FSL
+ tools which have defined their own command line arguments (see
+ loadFSLTool). Returns an object containing values for all of the
+ arguments that were passed in.
+ """
+
+ epilog = 'Type fslpy help <tool> for program-specific help. ' \
+ 'Available programs:\n {}'.format('\n '.join(allTools.keys()))
+
+ parser = argparse.ArgumentParser(
+ prog='fslpy',
+ description='Run a FSL program',
+ epilog=epilog,
+ formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument(
+ '-v', '--verbose', action='count',
+ help='Verbose output (can be used up to 3 times)')
+ parser.add_argument(
+ '-w', '--wxinspect', action='store_true',
+ help='Run wx inspection tool')
+ parser.add_argument('tool', help='FSL program to run')
+
+ # find the index of the first positional argument
+ try:
+ firstPos = map(lambda a: not a.startswith('-'), argv).index(True)
+ except ValueError:
+ firstPos = len(argv)
+
+ # Separate the top level arguments
+ # from the tool arguments, and parse
+ # the top level args
+ fslArgv = argv[:firstPos + 1]
+ toolArgv = argv[ firstPos + 1:]
+ namespace = parser.parse_args(fslArgv)
+
+ # if the specified tool is 'help', it should be followed by
+ # one more argument, the name of the tool to print help for
+ if namespace.tool == 'help':
+
+ # no tool name supplied
+ if len(toolArgv) == 0:
+ parser.print_help()
+ sys.exit(1)
+
+ # unknown tool name supplied
+ if toolArgv[0] not in allTools:
+ print '\nUnknown FSL tool: {}\n'.format(namespace.tool)
+ parser.print_help()
+ sys.exit(1)
+
+ fslTool = allTools[toolArgv[0]]
+
+ # no tool specific argument parser
+ if fslTool.parseArgs is None:
+ print 'No help for {}'.format(toolArgv[0])
+
+ # Otherwise, get help from the tool. We assume that
+ # all the argument parser for every tool will interpret
+ # '-h' as '--help', and will print some help
+ else:
+ fslTool.parseArgs(['-h'])
+ sys.exit(0)
+
+ # Unknown tool name supplied
+ elif namespace.tool not in allTools:
+ print '\nUnknown FSL tool: {}\n'.format(namespace.tool)
+ parser.print_help()
+ sys.exit(1)
+
+ # otherwise, give the remaining arguments to the tool parser
+ fslTool = allTools[namespace.tool]
+
+ if fslTool.parseArgs is not None: toolArgs = fslTool.parseArgs(toolArgv)
+ else: toolArgs = None
+
+ return fslTool, namespace, toolArgs
+
+
+def fslDirWarning(frame, toolName, fslEnvActive):
+ """
+ If fslEnvActive is False, displays a warning.
+ """
+
+ if fslEnvActive: return
+
+ msg = 'The FSLDIR environment variable is not set - '\
+ '{} may not behave correctly.'.format(toolName)
+
+ if frame is not None:
+ import wx
+ wx.MessageDialog(
+ frame,
+ message=msg,
+ style=wx.OK | wx.ICON_EXCLAMATION).ShowModal()
+ else:
+ log.warn(msg)
+
+
+def buildGUI(args, fslTool, toolCtx, fslEnvActive):
+ """
+ """
+
+ import wx
+ import fsl.utils.webpage as webpage
+
+ frame = fslTool.interface(None, args, toolCtx)
+
+ menuBar = frame.GetMenuBar()
+
+ if menuBar is None:
+ menuBar = wx.MenuBar()
+ frame.SetMenuBar(menuBar)
+
+ fslMenu = wx.Menu()
+ menuBar.Insert(0, fslMenu, 'FSL')
+
+ actions = []
+
+ actions.append((
+ wx.ID_HELP,
+ '{} Help'.format(fslTool.toolName),
+ lambda *ev: webpage.openFSLHelp(fslTool.helpPage)))
+
+ for (name, func) in fslTool.actions:
+ actions.append((wx.ID_ANY, name, lambda ev, f=func: f(frame, toolCtx)))
+
+ actions.append((
+ wx.ID_EXIT,
+ 'Exit',
+ lambda *ev: frame.Close()))
+
+ for wxId, name, func in actions:
+ menuItem = fslMenu.Append(wxId, name)
+ frame.Bind(wx.EVT_MENU, func, menuItem)
+
+ return frame
+
+
+def main():
+
+ fsldir = os.environ.get('FSLDIR', None)
+ fslEnvActive = fsldir is not None
+
+ allTools = loadAllFSLTools()
+ fslTool, args, toolArgs = parseArgs(sys.argv[1:], allTools)
+
+ if args.verbose == 1:
+ log.setLevel(logging.DEBUG)
+
+ # make some noisy things quiet
+ logging.getLogger('fsl.fslview.gl') .setLevel(logging.WARNING)
+ logging.getLogger('fsl.fslview.views').setLevel(logging.WARNING)
+ logging.getLogger('props') .setLevel(logging.WARNING)
+ logging.getLogger('pwidgets') .setLevel(logging.WARNING)
+ elif args.verbose == 2:
+ log.setLevel(logging.DEBUG)
+ logging.getLogger('props') .setLevel(logging.WARNING)
+ logging.getLogger('pwidgets').setLevel(logging.WARNING)
+ elif args.verbose == 3:
+ log.setLevel(logging.DEBUG)
+ logging.getLogger('props') .setLevel(logging.DEBUG)
+ logging.getLogger('pwidgets').setLevel(logging.DEBUG)
+
+ if fslTool.context is not None: ctx = fslTool.context(toolArgs)
+ else: ctx = None
+
+ if fslTool.interface is not None:
+ import wx
+ app = wx.App()
+ frame = buildGUI(toolArgs, fslTool, ctx, fslEnvActive)
+ frame.Show()
+
+ wx.CallLater(1, fslDirWarning, frame, fslTool.toolName, fslEnvActive)
+
+ if args.wxinspect:
+ import wx.lib.inspection
+ wx.lib.inspection.InspectionTool().Show()
+
+ app.MainLoop()
+
+ elif fslTool.execute is not None:
+ fslDirWarning( None, fslTool.toolName, fslEnvActive)
+ fslTool.execute(toolArgs, ctx)