/usr/bin/nib-ls is in python-nibabel 1.2.2-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 | #!/usr/bin/python
# 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.)
"""
__author__ = 'Yaroslav Halchenko'
__copyright__ = 'Copyright (c) 2011-2012 Yaroslav Halchenko ' \
'and NiBabel contributors'
__license__ = 'MIT'
import re
import sys
import nibabel as nib
import numpy as np
from math import ceil
from optparse import OptionParser, Option
from StringIO import StringIO
# global verbosity switch
verbose_level = 0
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 not align 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(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):
"""
"""
try:
f = getattr(obj, 'get_' + name)
return f()
except Exception, 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("-s", "--stats",
action="store_true", dest='stats', default=False,
help="Output basic data statistics"),
Option("-z", "--zeros",
action="store_true", dest='stats_zeros', default=False,
help="Include zeros into output basic data statistics (--stats)"),
])
return p
def proc_file(f, opts):
verbose(1, "Loading %s" % f)
row = ["@l%s" % f]
try:
vol = nib.load(f)
h = vol.get_header()
except Exception, 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 += [ '' ]
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, e:
verbose(2, "Failed to obtain qform or sform -- %s" % str(e))
if isinstance(h, nib.AnalyzeHeader):
row += ['']
else:
row += ['error']
if opts.stats:
# We are doomed to load data
try:
d = vol.get_data()
if not opts.stats_zeros:
d = d[np.nonzero(d)]
# just # of elements
row += ["[%d] " % np.prod(d.shape)]
# stats
row += [len(d) and '%.2g:%.2g' % (np.min(d), np.max(d)) or '-']
except Exception, e:
verbose(2, "Failed to obtain stats -- %s" % str(e))
row += ['error']
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()
|