python-nibabel 1.3.0-2 / usr / bin / nib-ls

#!/usr/bin/python
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#
#   See COPYING file distributed along with the NiBabel package for the
#   copyright and license terms.
#
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"""
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()