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Commit a57383e0 authored by Paul McCarthy's avatar Paul McCarthy
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Removed fsl.py - entry point is now in fsl/__init__.py

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#!/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)
fsl/__init__.py
+ 288
− 0
View file @ a57383e0
#!/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)
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