Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

329 lines (290 sloc) 10.31 kB
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""MultiVariate Pattern Analysis -- load helper
If you don't like to specify exact location of any particular
functionality within PyMVPA, please simply::
from mvpa2.suite import *
or
import mvpa2.suite
"""
__docformat__ = 'restructuredtext'
from mvpa2 import *
if __debug__ and 'SUITE' in debug.active:
__sdebug = lambda msg: debug('SUITE', "%s" % msg)
else:
__sdebug = lambda *args: None
__sdebug.__doc__ = "Shortcut to output debug messages for suite imports"
__sdebug('base')
from mvpa2.base import *
from mvpa2.base.attributes import *
from mvpa2.base.collections import *
from mvpa2.base.config import *
from mvpa2.base.dataset import *
from mvpa2.base.externals import *
from mvpa2.base.info import *
from mvpa2.base.types import *
from mvpa2.base.verbosity import *
from mvpa2.base.param import *
from mvpa2.base.state import *
from mvpa2.base.node import *
from mvpa2.base.learner import *
__sdebug('h5py')
if externals.exists('h5py'):
from mvpa2.base.hdf5 import *
__sdebug('reportlab')
if externals.exists('reportlab'):
from mvpa2.base.report import *
else:
from mvpa2.base.report_dummy import Report
__sdebug('algorithms')
from mvpa2.algorithms.hyperalignment import *
__sdebug('clfs')
from mvpa2 import clfs
__sdebug('clfs distance')
from mvpa2.clfs.distance import *
__sdebug('clfs base')
from mvpa2.clfs.base import *
__sdebug('clfs meta')
from mvpa2.clfs.meta import *
__sdebug('clfs kNN')
from mvpa2.clfs.knn import *
__sdebug('clfs lars')
if externals.exists('lars'):
from mvpa2.clfs.lars import *
__sdebug('clfs enet')
if externals.exists('elasticnet'):
from mvpa2.clfs.enet import *
__sdebug('clfs glmnet')
if externals.exists('glmnet'):
from mvpa2.clfs.glmnet import *
__sdebug('clfs skl')
if externals.exists('skl'):
if externals.versions['skl'] >= '0.9':
import sklearn as skl
else:
import scikits.learn as skl
from mvpa2.clfs.skl import *
__sdebug('clfs smlr')
from mvpa2.clfs.smlr import *
from mvpa2.clfs.blr import *
from mvpa2.clfs.gnb import *
from mvpa2.clfs.stats import *
from mvpa2.clfs.similarity import *
if externals.exists('libsvm') or externals.exists('shogun'):
__sdebug('clfs svm')
from mvpa2.clfs.svm import *
from mvpa2.clfs.transerror import *
__sdebug('clfs warehouse')
from mvpa2.clfs.warehouse import *
__sdebug('kernels')
from mvpa2 import kernels
from mvpa2.kernels.base import *
from mvpa2.kernels.np import *
if externals.exists('libsvm'):
from mvpa2.kernels.libsvm import *
if externals.exists('shogun'):
from mvpa2.kernels.sg import *
__sdebug('datasets')
from mvpa2 import datasets
from mvpa2.datasets import *
# just to make testsuite happy
from mvpa2.datasets.base import *
from mvpa2.datasets.formats import *
from mvpa2.datasets.miscfx import *
from mvpa2.datasets.eep import *
from mvpa2.datasets.eventrelated import *
if externals.exists('nibabel') :
from mvpa2.datasets.mri import *
__sdebug('generators')
from mvpa2.generators.base import *
from mvpa2.generators.partition import *
from mvpa2.generators.splitters import *
from mvpa2.generators.permutation import *
from mvpa2.generators.resampling import *
__sdebug('featsel')
from mvpa2 import featsel
from mvpa2.featsel.base import *
from mvpa2.featsel.helpers import *
from mvpa2.featsel.ifs import *
from mvpa2.featsel.rfe import *
__sdebug('mappers')
from mvpa2 import mappers
#from mvpa2.mappers import *
from mvpa2.mappers.base import *
from mvpa2.mappers.slicing import *
from mvpa2.mappers.flatten import *
from mvpa2.mappers.prototype import *
from mvpa2.mappers.projection import *
from mvpa2.mappers.svd import *
from mvpa2.mappers.procrustean import *
from mvpa2.mappers.boxcar import *
from mvpa2.mappers.fx import *
from mvpa2.mappers.fxy import *
from mvpa2.mappers.som import *
from mvpa2.mappers.zscore import *
if externals.exists('scipy'):
from mvpa2.mappers.detrend import *
from mvpa2.mappers.filters import *
if externals.exists('mdp'):
from mvpa2.mappers.mdp_adaptor import *
if externals.exists('mdp ge 2.4'):
from mvpa2.mappers.lle import *
__sdebug('measures')
from mvpa2 import measures
from mvpa2.measures.anova import *
if externals.exists('statsmodels'):
from mvpa2.measures.statsmodels_adaptor import *
from mvpa2.measures.irelief import *
from mvpa2.measures.base import *
from mvpa2.measures.noiseperturbation import *
from mvpa2.misc.neighborhood import *
from mvpa2.measures.searchlight import *
from mvpa2.measures.gnbsearchlight import *
from mvpa2.measures.corrstability import *
__sdebug('misc')
from mvpa2.support.copy import *
from mvpa2.misc.fx import *
from mvpa2.misc.attrmap import *
from mvpa2.misc.errorfx import *
from mvpa2.misc.cmdline import *
from mvpa2.misc.data_generators import *
from mvpa2.misc.exceptions import *
from mvpa2.misc import *
from mvpa2.misc.io import *
from mvpa2.misc.io.base import *
from mvpa2.misc.io.meg import *
if externals.exists('cPickle') and externals.exists('gzip'):
from mvpa2.misc.io.hamster import *
from mvpa2.misc.fsl import *
from mvpa2.misc.bv import *
from mvpa2.misc.bv.base import *
from mvpa2.misc.support import *
from mvpa2.misc.transformers import *
from mvpa2.misc.dcov import dCOV, dcorcoef
__sdebug("nibabel")
if externals.exists("nibabel"):
from mvpa2.misc.fsl.melodic import *
if externals.exists("pylab"):
from mvpa2.misc.plot import *
from mvpa2.misc.plot.erp import *
if externals.exists(['griddata', 'scipy']):
from mvpa2.misc.plot.topo import *
from mvpa2.misc.plot.lightbox import plot_lightbox
__sdebug("scipy dependents")
if externals.exists("scipy"):
from mvpa2.support.stats import scipy
from mvpa2.measures.corrcoef import *
from mvpa2.measures.ds import *
from mvpa2.clfs.ridge import *
from mvpa2.clfs.plr import *
from mvpa2.misc.stats import *
from mvpa2.clfs.gpr import *
from mvpa2.support.nipy import *
__sdebug("mappers wavelet")
if externals.exists("pywt"):
from mvpa2.mappers.wavelet import *
__sdebug("pylab")
if externals.exists("pylab"):
import pylab as pl
__sdebug("atlases")
if externals.exists("lxml") and externals.exists("nibabel"):
from mvpa2.atlases import *
__sdebug("ipython goodies")
if externals.exists("running ipython env"):
from mvpa2.support.ipython import *
ipy_activate_pymvpa_goodies()
def suite_stats():
"""Return cruel dict of things which evil suite provides
"""
glbls = globals()
import types
# Compatibility layer for Python3
try:
from io import FileIO as BuiltinFileType
except ImportError:
BuiltinFileType = types.FileType
try:
from types import ClassType as OldStyleClassType
except ImportError:
OldStyleClassType = type(None)
def _get_path(e):
"""Figure out basic path for the beast... probably there is already smth which could do that for me
"""
if str(e).endswith('(built-in)>'):
return "BUILTIN"
if hasattr(e, '__file__'):
return e.__file__
elif hasattr(e, '__path__'):
return e.__path__[0]
elif hasattr(e, '__module__'):
if isinstance(e.__module__, str):
return e.__module__
else:
return _get_path(e.__module__)
elif hasattr(e, '__class__'):
return _get_path(e.__class__)
else:
raise RuntimeError, "Could not figure out path for %s" % e
class EnvironmentStatistics(dict):
def __init__(self, d):
dict.__init__(self, foreign={})
# compute cruel stats
mvpa_str = '%smvpa' % os.path.sep
for k, e in d.iteritems():
found = False
for ty, tk, check_path in (
(list, "lists", False),
(str, "strings", False),
(unicode, "strings", False),
(BuiltinFileType, "files", False),
(types.BuiltinFunctionType, None, True),
(types.BuiltinMethodType, None, True),
(types.ModuleType, "modules", True),
(OldStyleClassType, "classes", True),
(type, "types", True),
(types.LambdaType, "functions", True),
(object, "objects", True),
):
if isinstance(e, ty):
found = True
if tk is None:
break
if not tk in self:
self[tk] = {}
if check_path:
mpath = _get_path(e)
if mvpa_str in mpath or mpath.startswith('mvpa2.'):
self[tk][k] = e
else:
self['foreign'][k] = e
else:
self[tk][k] = e
break
if not found:
raise ValueError, \
"Could not figure out placement for %s %s" % (k, e)
def __str__(self):
s = ""
for k in sorted(self.keys()):
s += "\n%s [%d entries]:" % (k, len(self[k]))
for i in sorted(self[k].keys()):
s += "\n %s" % i
# Lets extract first line in doc
try:
doc = self[k][i].__doc__.strip()
try:
ind = doc.index('\n')
except:
ind = 1000
s+= ": " + doc[:min(ind, 80)]
except:
pass
return s
return EnvironmentStatistics(globals())
__sdebug("THE END of mvpa2.suite imports")
Jump to Line
Something went wrong with that request. Please try again.