Merge branch 'master' into enh/norm_units

Author: effigies

bin/nib-ls

@@ -10,276 +10,8 @@
 """
 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))
+from nibabel.cmdline.ls import main
 
 
 if __name__ == '__main__':

nibabel/cmdline/__init__.py

@@ -0,0 +1,10 @@
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""Functionality to be exposed in the command line
+"""