RF - nib-ls is now functioning without PyMVPA with improved robustness

Author: yarikoptic

COPYING

@@ -24,6 +24,7 @@ documentation is covered by the MIT license.
   Copyright (c) 2006-2010 Michael Hanke <[email protected]>
   Copyright (c) 2011 Christian Haselgrove <[email protected]>
   Copyright (c) 2010-2011 Jarrod Millman <[email protected]>
+  Copyright (c) 2011-2012 Yaroslav Halchenko <[email protected]>
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal

bin/nib-ls

@@ -1,120 +1,227 @@
 #!/usr/bin/python
-#emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*- 
-#ex: set sts=4 ts=4 sw=4 noet:
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """
-Little script to list summary over given nifti files
-
- COPYRIGHT: Yaroslav Halchenko 2011
-
- LICENSE: MIT
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy
-  of this software and associated documentation files (the "Software"), to deal
-  in the Software without restriction, including without limitation the rights
-  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-  copies of the Software, and to permit persons to whom the Software is
-  furnished to do so, subject to the following conditions:
-
-  The above copyright notice and this permission notice shall be included in
-  all copies or substantial portions of the Software.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-  THE SOFTWARE.
+Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
 """
-#-----------------\____________________________________/------------------
 
 __author__ = 'Yaroslav Halchenko'
-__copyright__ = 'Copyright (c) 2011 Yaroslav Halchenko'
+__copyright__ = 'Copyright (c) 2011-2012 Yaroslav Halchenko ' \
+                'and NiBabel contributors'
 __license__ = 'MIT'
 
+import re
 import sys
-from mvpa2.base.dochelpers import table2string
-from mvpa2.base import verbose, debug
-from mvpa2.misc.cmdline import parser, opts, Option
+
 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'
 
-def ap(l, format, sep=', '):
-    """Little helper to enforce consistency"""
-    ls = [format % x for x in l]
-    return sep.join(ls)
-
-
-parser.usage = """Usage: %s [options] [infile1] [infile2] ...""" % sys.argv[0]
-parser.option_groups = [opts.common]
+            NspacesL = max(ceil((col_width[j] - len(item))/2.0), 0)
+            NspacesR = max(col_width[j] - NspacesL - len(item), 0)
 
-parser.add_options([
-    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)"),
-    ])
+            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
 
-(options, files) = parser.parse_args()
+            string_ += "%%%ds%%s%%%ds " \
+                       % (NspacesL, NspacesR) % ('', item, '')
+        string += string_.rstrip() + '\n'
+    out.write(string)
 
-if verbose.level < 3:
-    # suppress nibabel format-compliance warnings
-    nib.imageglobals.logger.level = 50
+    if print2string:
+        value = out.getvalue()
+        out.close()
+        return value
 
-if len(files):
-    maxfnlen = max([len(f) for f in files])
+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)
 
-    t = []
-    for f in files:
-        row = ["%%-%ds" % maxfnlen % f]
-        verbose(2, "Loading %s" % f)
-        try:
-            vol = nib.load(f)
-            h = vol.get_header()
-        except Exception, e:
-            row += ['failed']
-            t.append(row)
-            verbose(2, "Failed to gather information due to %s" % str(e))
-            continue
-        row += [ str(h.get_data_dtype()),
-                 '@l[%s]' %ap(h.get_data_shape(), '%3g'),
-                 '@l%s' % ap(h.get_zooms(), '%.2f', 'x') ]
-        # Slope
-        if (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()]
+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 += [ '' ]
-
-        if (hasattr(h, 'extensions') and len(h.extensions)):
-            row += ['@l#exts: %d' % len(h.extensions)]
+            row += ['']
+    except Exception, e:
+        verbose(2, "Failed to obtain qform or sform -- %s" % str(e))
+        if isinstance(h, nib.AnalyzeHeader):
+            row += ['']
         else:
-            row += [ '' ]
+            row += ['error']
 
+    if opts.stats:
+        # We are doomed to load data
         try:
-            if (h.get_qform() != h.get_sform()).any():
-                row += ['sform']
-            else:
-                row += ['']
-        except Exception, e:
-            verbose(2, "Failed to obtain qform or sform for %s due to %s" % (h, e))
-            if isinstance(h, nib.AnalyzeHeader):
-                row += ['']
-            else:
-                row += ['error']
-        if options.stats:
-            # We are doomed to load data
             d = vol.get_data()
-            if not options.stats_zeros:
+            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))
 
-        t.append(row)
 
-    print(table2string(t))
+if __name__ == '__main__':
+    main()