class TestRexTagger(unittest.TestCase):
def setUp(self):
self.tagger = RexTagger('foo', [
r'foo',
])
def test_match(self):
text = 'foo bar baz'
tag = self.tagger.tag(text)
assert_equal(
tag,
Tag({
'label': 'foo',
'context': 'foo bar baz',
'span': (0, 3),
}))
'eprime',
[
r'\We{dlm}prime'.format(dlm=delimiter),
],
version_separator,
looks=Looks(negahead=r'(\w|\.[1-9])'),
versions=[
'1',
'1.1',
'1.2',
'2',
],
)
presentation = RexTagger('presentation', [
r'neuro{dlm}bs'.format(dlm=delimiter),
r'neuro{dlm}behavioral{dlm}systems'.format(dlm=delimiter),
])
psychtoolbox = RexTagger('psychtoolbox', [
r'psychtoolbox',
r'psychophysics{dlm}toolbox'.format(dlm=delimiter),
])
psychopy = RexTagger('psychopy', [
r'\Wpsychopy\W',
])
visionegg = RexTagger('visionegg', [
r'vision{dlm}egg'.format(dlm=delimiter),
])
version_separator,
arbitrary_rex=r'(?P<version>\d(\.\d)+)',
post_proc=post_proc,
)
voyager = RexComboVersionTagger(
'voyager',
[r'brain{dlm}voyager{dlm}(2000|qx)?'.format(dlm=delimiter)],
version_separator,
arbitrary_rex=r'(?P<version>\d\.\d)',
post_proc=post_proc,
)
suma = RexTagger(
'suma',
[
r'\Wsuma\W',
],
)
medx = RexTagger(
'medx',
[
r'\Wmedx[^a-z]',
],
)
caret = RexTagger(
'caret',
[
r'caret', r'surefit', r'''
computerized{dlm}anatomical{dlm}reconstruction{dlm}
category = 'analysis'
from neurotrends.tagger import RexTagger, MultiRexTagger
from .misc import delimiter
from neurotrends.config import re
event = RexTagger(
'event',
[
r'null{dlm}event'.format(dlm=delimiter),
r'null{dlm}trial'.format(dlm=delimiter),
r'fixation{dlm}event'.format(dlm=delimiter),
r'fixation{dlm}trial'.format(dlm=delimiter),
r'''
separating{dlm}processes{dlm}within{dlm}a{dlm}trial{dlm}in{dlm}
event{dlm}related{dlm}functional{dlm}mri
'''.format(dlm=delimiter),
r'''
a{dlm}trial{dlm}based{dlm}experimental{dlm}design{dlm}for{dlm}fmri
'''.format(dlm=delimiter),
]
)
event_context = MultiRexTagger(
'event',
[
r'event{dlm}related{dlm}design'.format(dlm=delimiter),
r'event{dlm}related{dlm}analysis'.format(dlm=delimiter),
r'event{dlm}related{dlm}fmri'.format(dlm=delimiter),
r'event{dlm}related{dlm}task'.format(dlm=delimiter),
# -*- coding: utf-8 -*-
category = 'tool'
import os
from neurotrends.config import re
from neurotrends.tagger import Looks, RexTagger, RexComboVersionTagger
from neurotrends.pattern.misc import delimiter, version_separator
from neurotrends import trendpath
from .matlab_utils import get_versions, get_version_regexes
python = RexTagger('python', [r'python'])
java = RexTagger('java', [
r'java(?!{dlm}script)'.format(dlm=delimiter),
])
rlang = RexTagger('rlang', [
r'\Wr{dlm}project'.format(dlm=delimiter),
r'\Wr{dlm}development{dlm}(core)?{dlm}team'.format(dlm=delimiter),
r'''
\Wr{dlm}foundation{dlm}for{dlm}statistical{dlm}computing
'''.format(dlm=delimiter),
r'''
(software|programming){dlm}(language|environment){dlm}r(?!\w)
'''.format(dlm=delimiter),
r'''
\Wr{dlm}(software|programming){dlm}(language|senvironment)
'''.format(dlm=delimiter),
"""
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from ..misc import delimiter, float_ptn, mov_ptn, cor_ptn
num_ptn = r'\d*\.?\d+'
mm_ptn = r'(mm|milli{dlm}met(er|re)s?)'.format(dlm=delimiter)
fw_ptn = r'(fwhm|full{dlm}width)'.format(dlm=delimiter)
hm_ptn = r'(fwhm|half{dlm}max(imum)?)'.format(dlm=delimiter)
power = RexTagger(
'power',
[
r'power{dlm}analysis'.format(dlm=delimiter),
r'power{dlm}calculation'.format(dlm=delimiter),
r'sample{dlm}size{dlm}calculation'.format(dlm=delimiter),
]
)
desopt = RexTagger(
'desopt',
[
r'design{dlm}optimi[sz]ation'.format(dlm=delimiter),
r'optimization{dlm}of{dlm}experimental{dlm}design'.format(
dlm=delimiter
),
r'\Wm{dlm}sequence'.format(dlm=delimiter),
r'optseq',
]
)
def setUp(self):
self.tagger = RexTagger('foo', [
r'foo',
])
category = 'analysis'
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from misc import delimiter
fdr = RexTagger('fdr', [
r'false{dlm}discovery{dlm}rate'.format(dlm=delimiter),
r'\Wfdr\W',
])
fwe = RexTagger('fwe', [
r'family{dlm}wise{dlm}error'.format(dlm=delimiter),
r'\Wfwe\w',
])
rft = RexTagger(
'rft',
[
r'random{dlm}field{dlm}theory'.format(dlm=delimiter),
r'gaussian{dlm}random{dlm}field'.format(dlm=delimiter),
r'\Wgrf{dlm}theory'.format(dlm=delimiter),
r'theory{dlm}of{dlm}random{dlm}fields'.format(dlm=delimiter),
# Worsley et al., 1992
r'''
a{dlm}three{dlm}dimensional{dlm}statistical{dlm}analysis{dlm}
for{dlm}cbf{dlm}activation{dlm}studies{dlm}in{dlm}human
{dlm}brain
'''.format(dlm=delimiter),
# Friston et al., 1994
r'''
cat = 'analysis'
from neurotrends.tagger import RexTagger
from misc import delimiter, mni_ptn, mni_num_ptn, spc_ptn
mni = RexTagger('mni', [
mni_num_ptn + delimiter + spc_ptn,
r'{spc}{dlm}of{dlm}the{dlm}{mni}'.format(
spc=spc_ptn,
mni=mni_ptn,
dlm=delimiter,
),
])
tal = RexTagger('tal', [
r'talairach{dlm}{spc}'.format(
spc=spc_ptn,
dlm=delimiter,
),
])
category = 'tool'
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from misc import delimiter
### Sequences ###
mprage = RexTagger('mprage', [
r'\Wmp{dlm}rage\W'.format(dlm=delimiter),
])
spgr = RexTagger('spgr', [
r'\Wspgr\W',
])
### Trajectories ###
epi = RexTagger('epi', [
r'echo{dlm}planar'.format(dlm=delimiter),
re.compile(r'EPI'),
])
spiral = RexTagger('spiral', [
r'spiral{dlm}in'.format(dlm=delimiter),
r'spiral{dlm}out'.format(dlm=delimiter),
])
spiral_context = MultiRexTagger('spiral', [
r'spiral',
from neurotrends.tagger import RexTagger, MultiRexTagger
from misc import delimiter
os_secondary_ptn = [
r'\Wpc\W',
r'\Wos\W',
r'operating',
r'platform',
r'environment',
r'workstation',
]
mac = RexTagger(
'mac',
[
re.compile(r'OS[-/\s]*X'),
r'\Wmac{dlm}os\W'.format(dlm=delimiter),
r'spss{dlm}for{dlm}mac'.format(dlm=delimiter),
]
)
mac_context = MultiRexTagger(
'mac',
[
r'apple',
r'mac(intosh)?',
],
os_secondary_ptn,
separator='[^.,:;?]*'
)
windows_context = MultiRexTagger(
# -*- coding: utf-8 -*-
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from ..misc import delimiter
ge = RexTagger('ge', [
r'general{dlm}electric'.format(dlm=delimiter),
])
# Use MultiRexTagger for GE to disambiguate names: e.g. GE Smith
ge_context = MultiRexTagger('ge', [
re.compile(r'\bGE\b'),
], [
r'mri',
r'scan',
r'tesla',
])
siemens = RexTagger('siemens', [r'siemens'])
philips = RexTagger('philips', [r'philips'])
bruker = RexTagger('bruker', [r'bruker'])
varian = RexTagger('varian', [r'varian\W'])
shimazdu = RexTagger('shimadzu', [r'shimazdu'])
marconi = RexTagger('marconi', [r'marconi'])
category = 'tool'
from neurotrends.config import re
from neurotrends.tagger import RexTagger
from misc import delimiter, mni_ptn, spc_ptn
marsbar = RexTagger('marsbar', [
r'mars{dlm}bar'.format(dlm=delimiter),
r'sourceforge\.net/projects/marsbar',
r'''
marseille{dlm}region{dlm}of{dlm}interest{dlm}toolbox
'''.format(dlm=delimiter),
])
pickatlas = RexTagger('pickatlas', [
r'\Wpick{dlm}atlas'.format(dlm=delimiter),
])
surfrend = RexTagger('surfrend', [
r'\Wsurf{dlm}rend'.format(dlm=delimiter),
])
rest = RexTagger('rest', [
r'resting{dlm}state{dlm}fmri{dlm}data{dlm}analysis{dlm}toolkit'.format(
dlm=delimiter),
r'rest{dlm}(by)?{dlm}song{dlm}xiao'.format(dlm=delimiter),
r'resting\-fmri\.sourceforge\.net',
r'sourceforge\.net/projects/resting\-fmri',
r'restfmri\.net',
])
category = 'analysis'
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from misc import delimiter
syn_ptn = r'(spm|canonical|standard|synthetic|reference|(proto)?typical)'
hrf_ptn = r'(hrf|hdr|ha?emodynamic{dlm}(impulse)?{dlm}response)'.format(
dlm=delimiter)
selavg = RexTagger('selavg', [
r'selective(ly)?{dlm}averag'.format(dlm=delimiter),
])
hrf = RexTagger('hrf', [
syn_ptn + delimiter + hrf_ptn,
r'''
convol(ved?|ution){dlm}with{dlm}(an?|the){dlm}
{syn}?{dlm}{hrf}
'''.format(
syn=syn_ptn,
hrf=hrf_ptn,
dlm=delimiter,
),
r'gamma{dlm}{hrf}'.format(
hrf=hrf_ptn,
dlm=delimiter,
),
r'(single|first|positive){dlm}gamma{dlm}function'.format(dlm=delimiter),
r'(double|second){dlm}gamma'.format(dlm=delimiter),
category = 'analysis'
from neurotrends.config import re
from neurotrends.tagger import RexTagger, MultiRexTagger
from misc import delimiter
kda = RexTagger(
'kda',
[
re.compile(r'\WKDA\W'),
]
)
kda_context = MultiRexTagger(
'kda',
[
r'kernel{dlm}density{dlm}analysis'.format(dlm=delimiter),
],
[
r'multi{dlm}level'.format(dlm=delimiter),
],
separator='[^.,:;?]*'
)
mkda = RexTagger(
'mkda',
[
r'''
multi{dlm}level{dlm}kernel{dlm}density{dlm}analysis
'''.format(dlm=delimiter),
r'multi{dlm}level{dlm}kda'.format(dlm=delimiter),