def est_smooth_kernel(txt):
# Initialize FWHM
kernels = []
ctxt = re.sub(r'[():=]', '', txt)
for ptn in smooth_spatial_ptn:
matches = rex_flex(ptn, ctxt, re.finditer)
for match in matches:
kernel_str = match.groupdict()['kernel']
# Handle ...
six_match = re.search('(\d+?)6(\d+?)6(\d+)', kernel_str)
if six_match:
if len(set(six_match.groups())) == 1:
kernel_str = six_match.groups()[-1]
# Skip if match preceded by number; prevents matches on input like
# "6 .5 mm fwhm"
context_back, _ = rex_ctx(match, ctxt, nchar_pre=10, nchar_post=0)
before_group = context_back.replace(match.group(), '')
if re.search(r'[.\d]\s+$', before_group):
continue
# Skip if not float
try:
kernel = float(kernel_str)
except (ValueError, TypeError):
continue
# Skip if implausible
if kernel > MAX_FWHM:
continue
context, span = rex_ctx(match, ctxt)
group = match.group()
kernels.append({
'value': kernel,
'context': context,
'group': group,
'span': span,
})
return kernels
def est_smooth_kernel(txt):
# Initialize FWHM
kernels = []
ctxt = re.sub(r'[():=]', '', txt)
for ptn in smooth_spatial_ptn:
matches = rex_flex(ptn, ctxt, re.finditer)
for match in matches:
kernel_str = match.groupdict()['kernel']
# Handle ...
six_match = re.search('(\d+?)6(\d+?)6(\d+)', kernel_str)
if six_match:
if len(set(six_match.groups())) == 1:
kernel_str = six_match.groups()[-1]
# Skip if match preceded by number; prevents matches on input like
# "6 .5 mm fwhm"
context_back, _ = rex_ctx(match, ctxt, nchar_pre=10, nchar_post=0)
before_group = context_back.replace(match.group(), '')
if re.search(r'[.\d]\s+$', before_group):
continue
# Skip if not float
try:
kernel = float(kernel_str)
except (ValueError, TypeError):
continue
# Skip if implausible
if kernel > MAX_FWHM:
continue
context, span = rex_ctx(match, ctxt)
group = match.group()
kernels.append({
'value': kernel,
'context': context,
'group': group,
'span': span,
})
return kernels
def test_nchar_post_zero(self):
"""Regression test. Check for bug by which `nchar_post=0` is equivalent
to `nchar_post=None`.
"""
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_post=0)
assert_equal(result[0], 'foo bar')
assert_equal(result[1], (4, 7))
def test_nchar_post(self):
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_post=2)
assert_equal(
result[0],
'foo bar b'
)
assert_equal(
result[1],
(4, 7)
)
def test_nchar_pre(self):
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_pre=2)
assert_equal(
result[0],
'o bar baz'
)
assert_equal(
result[1],
(4, 7)
)
def est_field_strength(txt):
fields = []
for ptn in field_ptn:
matches = rex_flex(ptn, txt, fun=re.finditer)
for match in matches:
short_context, _ = rex_ctx(match=match, txt=txt, nchar=50)
if not re.search(mag_ptn, short_context, re.I):
continue
# Skip if significance test; easy to confuse with e.g.
# "3.0 T, p < 0.05"
post_context, _ = rex_ctx(match, txt, nchar_pre=0, nchar_post=50)
if rex_flex(sig_ptn, post_context):
continue
field_str = match.groupdict()['field']
# Try to cast field strength to float
try:
field = float(field_str)
except (ValueError, TypeError):
continue
if MIN_FIELD_STRENGTH <= field <= MAX_FIELD_STRENGTH:
context, span = rex_ctx(match, txt)
group = match.group()
fields.append({
'value': field,
'context': context,
'group': group,
'span': span,
})
return fields
def est_field_strength(txt):
fields = []
for ptn in field_ptn:
matches = rex_flex(ptn, txt, fun=re.finditer)
for match in matches:
short_context, _ = rex_ctx(match=match, txt=txt, nchar=50)
if not re.search(mag_ptn, short_context, re.I):
continue
# Skip if significance test; easy to confuse with e.g.
# "3.0 T, p < 0.05"
post_context, _ = rex_ctx(match, txt, nchar_pre=0, nchar_post=50)
if rex_flex(sig_ptn, post_context):
continue
field_str = match.groupdict()['field']
# Try to cast field strength to float
try:
field = float(field_str)
except (ValueError, TypeError):
continue
if MIN_FIELD_STRENGTH <= field <= MAX_FIELD_STRENGTH:
context, span = rex_ctx(match, txt)
group = match.group()
fields.append({
'value': field,
'context': context,
'group': group,
'span': span,
})
return fields
def test_nchar_post_zero(self):
"""Regression test. Check for bug by which `nchar_post=0` is equivalent
to `nchar_post=None`.
"""
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_post=0)
assert_equal(
result[0],
'foo bar'
)
assert_equal(
result[1],
(4, 7)
)
def est_highpass_cutoff(txt):
"""
"""
cutoffs = []
ctxt = re.sub('[():=]', '', txt)
for ptn in highpass_filter_bool_ptn:
matches = rex_flex(ptn, ctxt, re.finditer)
for match in matches:
context, span = rex_ctx(match, ctxt)
# Skip if negative patterns match
stop = False
for neg_ptn in highpass_filter_neg_ptn:
if rex_flex(neg_ptn, context):
stop = True
break
if stop:
continue
# Skip if wide-range negative patterns match
context_wide, _ = rex_ctx(match, ctxt, nchar=500)
for neg_ptn in highpass_filter_wide_neg_ptn:
if rex_flex(neg_ptn, context_wide):
stop = True
break
if stop:
continue
context_search, _ = rex_ctx(match, ctxt, nchar_pre=0)
# Match on fraction pattern (e.g. 1 / 128 Hz)
matches = rex_flex(
highpass_filter_values_fraction, context_search,
fun=re.finditer
)
matches = list(matches)
if len(matches) == 1:
match = matches[0]
group = match.group()
numerator = match.groupdict()['num']
denominator = match.groupdict()['dnm']
if (numerator.startswith('0') and not numerator.startswith('0.')) or \
(denominator.startswith('0') and not denominator.startswith('0.')):
continue
try:
numerator = float(numerator)
denominator = float(denominator)
except (ValueError, TypeError):
continue
# Avoid zero-division errors
if numerator == 0 or denominator == 0:
continue
cutoff = numerator / denominator
units = match.groupdict()['units']
if units.lower() == 'hz':
cutoff = 1 / cutoff
cutoffs.append({
'value': cutoff,
'context': context,
'group': group,
'span': span,
})
# Stop if fraction matches
continue
# Match on single-value pattern (e.g. 0.05 Hz)
matches = rex_flex(
highpass_filter_values, context_search, fun=re.finditer
)
matches = list(matches)
if len(matches) == 1:
match = matches[0]
group = match.group()
cutoff = match.groupdict()['cutoff']
if cutoff.startswith('0') and not cutoff.startswith('0.'):
continue
try:
cutoff = float(cutoff)
except (ValueError, TypeError):
continue
if cutoff == 0:
continue
units = match.groupdict()['units']
if units.lower() == 'hz':
cutoff = 1 / cutoff
cutoffs.append({
'value': cutoff,
'context': context,
'group': group,
'span': span,
})
return cutoffs
def test_nchar_post(self):
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_post=2)
assert_equal(result[0], 'foo bar b')
assert_equal(result[1], (4, 7))
def test_nchar_pre(self):
result = rex_ctx(txt=self.text, ptn=self.pattern, nchar_pre=2)
assert_equal(result[0], 'o bar baz')
assert_equal(result[1], (4, 7))
def test_nomatch(self):
result = rex_ctx(txt=self.text, ptn=self.pattern)
assert_equal(result[0], self.text)
assert_equal(result[1], (4, 7))
def test_match(self):
match = rex_flex(self.pattern, self.text)
result = rex_ctx(match, self.text)
assert_equal(result[0], self.text)
assert_equal(result[1], ((4, 7)))
def test_nomatch(self):
result = rex_ctx(txt=self.text, ptn=self.pattern)
assert_equal(result[0], self.text)
assert_equal(result[1], (4, 7))
def test_match(self):
match = rex_flex(self.pattern, self.text)
result = rex_ctx(match, self.text)
assert_equal(result[0], self.text)
assert_equal(result[1], ((4, 7)))
def est_highpass_cutoff(txt):
"""
"""
cutoffs = []
ctxt = re.sub(r'[():=]', '', txt)
for ptn in highpass_filter_bool_ptn:
matches = rex_flex(ptn, ctxt, re.finditer)
for match in matches:
context, span = rex_ctx(match, ctxt)
# Skip if negative patterns match
stop = False
for neg_ptn in highpass_filter_neg_ptn:
if rex_flex(neg_ptn, context):
stop = True
break
if stop:
continue
# Skip if wide-range negative patterns match
context_wide, _ = rex_ctx(match, ctxt, nchar=500)
for neg_ptn in highpass_filter_wide_neg_ptn:
if rex_flex(neg_ptn, context_wide):
stop = True
break
if stop:
continue
context_search, _ = rex_ctx(match, ctxt, nchar_pre=0)
# Match on fraction pattern (e.g. 1 / 128 Hz)
matches = rex_flex(highpass_filter_values_fraction,
context_search,
fun=re.finditer)
matches = list(matches)
if len(matches) == 1:
match = matches[0]
group = match.group()
numerator = match.groupdict()['num']
denominator = match.groupdict()['dnm']
if (numerator.startswith('0') and not numerator.startswith('0.')) or \
(denominator.startswith('0') and not denominator.startswith('0.')):
continue
try:
numerator = float(numerator)
denominator = float(denominator)
except (ValueError, TypeError):
continue
# Avoid zero-division errors
if numerator == 0 or denominator == 0:
continue
cutoff = numerator / denominator
units = match.groupdict()['units']
if units.lower() == 'hz':
cutoff = 1 / cutoff
cutoffs.append({
'value': cutoff,
'context': context,
'group': group,
'span': span,
})
# Stop if fraction matches
continue
# Match on single-value pattern (e.g. 0.05 Hz)
matches = rex_flex(highpass_filter_values,
context_search,
fun=re.finditer)
matches = list(matches)
if len(matches) == 1:
match = matches[0]
group = match.group()
cutoff = match.groupdict()['cutoff']
if cutoff.startswith('0') and not cutoff.startswith('0.'):
continue
try:
cutoff = float(cutoff)
except (ValueError, TypeError):
continue
if cutoff == 0:
continue
units = match.groupdict()['units']
if units.lower() == 'hz':
cutoff = 1 / cutoff
cutoffs.append({
'value': cutoff,
'context': context,
'group': group,
'span': span,
})
return cutoffs
