/usr/bin/nib-ls is in python-nibabel 2.2.1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# emacs: -*- mode: python-mode; 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 NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""
Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
"""
from __future__ import division, print_function, absolute_import
import re
import sys
import numpy as np
import nibabel as nib
from math import ceil
from optparse import OptionParser, Option
from io import StringIO
from nibabel.py3k import asunicode
__author__ = 'Yaroslav Halchenko'
__copyright__ = 'Copyright (c) 2011-2016 Yaroslav Halchenko ' \
'and NiBabel contributors'
__license__ = 'MIT'
# global verbosity switch
verbose_level = 0
MAX_UNIQUE = 1000 # maximal number of unique values to report for --counts
def _err(msg=None):
"""To return a string to signal "error" in output table"""
if msg is None:
msg = 'error'
return '!' + msg
def verbose(l, msg):
"""Print `s` if `l` is less than the `verbose_level`
"""
# TODO: consider using nibabel's logger
if l <= int(verbose_level):
print("%s%s" % (' ' * l, msg))
def error(msg, exit_code):
print >> sys.stderr, msg
sys.exit(exit_code)
def table2string(table, out=None):
"""Given list of lists figure out their common widths and print to out
Parameters
----------
table : list of lists of strings
What is aimed to be printed
out : None or stream
Where to print. If None -- will print and return string
Returns
-------
string if out was None
"""
print2string = out is None
if print2string:
out = StringIO()
# equalize number of elements in each row
nelements_max = \
len(table) and \
max(len(x) for x in table)
for i, table_ in enumerate(table):
table[i] += [''] * (nelements_max - len(table_))
# figure out lengths within each column
atable = np.asarray(table)
# eat whole entry while computing width for @w (for wide)
markup_strip = re.compile('^@([lrc]|w.*)')
col_width = [max([len(markup_strip.sub('', x))
for x in column]) for column in atable.T]
string = ""
for i, table_ in enumerate(table):
string_ = ""
for j, item in enumerate(table_):
item = str(item)
if item.startswith('@'):
align = item[1]
item = item[2:]
if align not in ['l', 'r', 'c', 'w']:
raise ValueError('Unknown alignment %s. Known are l,r,c' %
align)
else:
align = 'c'
nspacesl = max(ceil((col_width[j] - len(item)) / 2.0), 0)
nspacesr = max(col_width[j] - nspacesl - len(item), 0)
if align in ['w', 'c']:
pass
elif align == 'l':
nspacesl, nspacesr = 0, nspacesl + nspacesr
elif align == 'r':
nspacesl, nspacesr = nspacesl + nspacesr, 0
else:
raise RuntimeError('Should not get here with align=%s' % align)
string_ += "%%%ds%%s%%%ds " \
% (nspacesl, nspacesr) % ('', item, '')
string += string_.rstrip() + '\n'
out.write(asunicode(string))
if print2string:
value = out.getvalue()
out.close()
return value
def ap(l, format_, sep=', '):
"""Little helper to enforce consistency"""
if l == '-':
return l
ls = [format_ % x for x in l]
return sep.join(ls)
def safe_get(obj, name):
"""A getattr which would return '-' if getattr fails
"""
try:
f = getattr(obj, 'get_' + name)
return f()
except Exception as e:
verbose(2, "get_%s() failed -- %s" % (name, e))
return '-'
def get_opt_parser():
# use module docstring for help output
p = OptionParser(
usage="%s [OPTIONS] [FILE ...]\n\n" % sys.argv[0] + __doc__,
version="%prog " + nib.__version__)
p.add_options([
Option("-v", "--verbose", action="count",
dest="verbose", default=0,
help="Make more noise. Could be specified multiple times"),
Option("-H", "--header-fields",
dest="header_fields", default='',
help="Header fields (comma separated) to be printed as well (if present)"),
Option("-s", "--stats",
action="store_true", dest='stats', default=False,
help="Output basic data statistics"),
Option("-c", "--counts",
action="store_true", dest='counts', default=False,
help="Output counts - number of entries for each numeric value "
"(useful for int ROI maps)"),
Option("--all-counts",
action="store_true", dest='all_counts', default=False,
help="Output all counts, even if number of unique values > %d" % MAX_UNIQUE),
Option("-z", "--zeros",
action="store_true", dest='stats_zeros', default=False,
help="Include zeros into output basic data statistics (--stats, --counts)"),
])
return p
def proc_file(f, opts):
verbose(1, "Loading %s" % f)
row = ["@l%s" % f]
try:
vol = nib.load(f)
h = vol.header
except Exception as e:
row += ['failed']
verbose(2, "Failed to gather information -- %s" % str(e))
return row
row += [str(safe_get(h, 'data_dtype')),
'@l[%s]' % ap(safe_get(h, 'data_shape'), '%3g'),
'@l%s' % ap(safe_get(h, 'zooms'), '%.2f', 'x')]
# Slope
if hasattr(h, 'has_data_slope') and \
(h.has_data_slope or h.has_data_intercept) and \
not h.get_slope_inter() in [(1.0, 0.0), (None, None)]:
row += ['@l*%.3g+%.3g' % h.get_slope_inter()]
else:
row += ['']
if hasattr(h, 'extensions') and len(h.extensions):
row += ['@l#exts: %d' % len(h.extensions)]
else:
row += ['']
if opts.header_fields:
# signals "all fields"
if opts.header_fields == 'all':
# TODO: might vary across file types, thus prior sensing
# would be needed
header_fields = h.keys()
else:
header_fields = opts.header_fields.split(',')
for f in header_fields:
if not f: # skip empty
continue
try:
row += [str(h[f])]
except (KeyError, ValueError):
row += [_err()]
try:
if (hasattr(h, 'get_qform') and hasattr(h, 'get_sform') and
(h.get_qform() != h.get_sform()).any()):
row += ['sform']
else:
row += ['']
except Exception as e:
verbose(2, "Failed to obtain qform or sform -- %s" % str(e))
if isinstance(h, nib.AnalyzeHeader):
row += ['']
else:
row += [_err()]
if opts.stats or opts.counts:
# We are doomed to load data
try:
d = vol.get_data()
if not opts.stats_zeros:
d = d[np.nonzero(d)]
else:
# at least flatten it -- functionality below doesn't
# depend on the original shape, so let's use a flat view
d = d.reshape(-1)
if opts.stats:
# just # of elements
row += ["@l[%d]" % np.prod(d.shape)]
# stats
row += [len(d) and '@l[%.2g, %.2g]' % (np.min(d), np.max(d)) or '-']
if opts.counts:
items, inv = np.unique(d, return_inverse=True)
if len(items) > 1000 and not opts.all_counts:
counts = _err("%d uniques. Use --all-counts" % len(items))
else:
freq = np.bincount(inv)
counts = " ".join("%g:%d" % (i, f) for i, f in zip(items, freq))
row += ["@l" + counts]
except IOError as e:
verbose(2, "Failed to obtain stats/counts -- %s" % str(e))
row += [_err()]
return row
def main():
"""Show must go on"""
parser = get_opt_parser()
(opts, files) = parser.parse_args()
global verbose_level
verbose_level = opts.verbose
if verbose_level < 3:
# suppress nibabel format-compliance warnings
nib.imageglobals.logger.level = 50
rows = [proc_file(f, opts) for f in files]
print(table2string(rows))
if __name__ == '__main__':
main()
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