# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Unit tests for PyMVPA verbose and debug output"""
import unittest, re
from StringIO import StringIO
from mvpa2.base.verbosity import OnceLogger
from mvpa2.base import verbose, error
if __debug__:
from mvpa2.base import debug
debug.register('1', 'id 1') # needed for testing
debug.register('2', 'id 2')
## XXX There must be smth analogous in python... don't know it yet
# And it is StringIO
#class StringStream(object):
# def __init__(self):
# self.__str = ""
#
# def __repr__(self):
# return self.__str
#
# def write(self, s):
# self.__str += s
#
from mvpa2.support.nibabel import surf
from mvpa2.base.progress import ProgressBar, seconds2prettystring
if externals.exists('h5py'):
from mvpa2.base.hdf5 import h5save, h5load
# TODO: see if we use these contants, or let it be up to the user
# possibly also rename them
LINEAR_VOXEL_INDICES = "linear_voxel_indices"
CENTER_DISTANCES = "center_distances"
GREY_MATTER_POSITION = "grey_matter_position"
from mvpa2.base import debug
if __debug__:
if not "SVS" in debug.registered:
debug.register("SVS", "Surface-based voxel selection "
" (a.k.a. 'surfing')")
class VoxelSelector(object):
'''Voxel selection for surface-based searchlights'''
def __init__(self,
radius,
distance_surf,
n2v,
distance_metric='dijkstra',
outside_node_margin=None):
'''
Voxel selection using cortical surfaces.
Parameters
----------
from mvpa2.base.progress import ProgressBar, seconds2prettystring
if externals.exists('h5py'):
from mvpa2.base.hdf5 import h5save, h5load
# TODO: see if we use these contants, or let it be up to the user
# possibly also rename them
LINEAR_VOXEL_INDICES = "linear_voxel_indices"
CENTER_DISTANCES = "center_distances"
GREY_MATTER_POSITION = "grey_matter_position"
from mvpa2.base import debug
if __debug__:
if not "SVS" in debug.registered:
debug.register("SVS", "Surface-based voxel selection "
" (a.k.a. 'surfing')")
class VoxelSelector(object):
'''Voxel selection for surface-based searchlights'''
def __init__(self, radius, distance_surf, n2v, distance_metric='dijkstra',
outside_node_margin=None):
'''
Voxel selection using cortical surfaces.
Parameters
----------
radius: int or float
Searchlight radius. If the type is int, then this set the number of
voxels in each searchlight (with variable size of the disc across
searchlights). If the type is float, then this sets the disc radius in
WiP
TODO: some nice refactoring of the code. Currently it's a bit of
a mess.
'''
import re, numpy as np, random, os, time, sys, base64, copy, math
from io import BytesIO
from mvpa2.support.nibabel import afni_niml_types as types
_RE_FLAGS = re.DOTALL # regular expression matching spans across new lines
from mvpa2.base import debug
if __debug__:
if not "NIML" in debug.registered:
debug.register("NIML", "NeuroImaging Markup Language")
_TEXT_ROWSEP = "\n"
_TEXT_COLSEP = " "
# define NIML specific escape characters
_ESCAPE = {
'<': '<',
'>': '>',
'"': '"',
'&': '&',
''': "'"
}
def decode_escape(s):
WiP
TODO: some nice refactoring of the code. Currently it's a bit of
a mess.
'''
import re, numpy as np, random, os, time, sys, base64, copy, math
from io import BytesIO
from mvpa2.support.nibabel import afni_niml_types as types
_RE_FLAGS = re.DOTALL # regular expression matching spans across new lines
from mvpa2.base import debug
if __debug__:
if not "NIML" in debug.registered:
debug.register("NIML", "NeuroImaging Markup Language")
_TEXT_ROWSEP = "\n"
_TEXT_COLSEP = " "
# define NIML specific escape characters
_ESCAPE = {'<':'<',
'>':'>',
'"':'"',
'&':'&',
''':"'"}
def decode_escape(s):
for k, v in _ESCAPE.iteritems():
s = s.replace(k, v)
return s
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Unit tests for PyMVPA verbose and debug output"""
import unittest, re
from StringIO import StringIO
from mvpa2.base.verbosity import OnceLogger
from mvpa2.base import verbose, error
if __debug__:
from mvpa2.base import debug
debug.register('1', 'id 1') # needed for testing
debug.register('2', 'id 2')
## XXX There must be smth analogous in python... don't know it yet
# And it is StringIO
#class StringStream(object):
# def __init__(self):
# self.__str = ""
#
# def __repr__(self):
# return self.__str
#
# def write(self, s):
# self.__str += s
#
