Merge pull request #348 from yarikoptic/nibls-header

MRG: add -H for nib-ls to list desired header fields

saw https://neurostars.org/p/3361/ which triggered to do this tiny hack (time for tests for the beast will come!)

Now it should be possible to specify some header fields desired to be output, which will get listed as well, e.g.:

```
$> $PWD/bin/nib-ls -H dim,bitpix /usr/share/data/fsl-mni152-templates/MNI152*brain.nii.gz
/usr/share/data/fsl-mni152-templates/MNI152lin_T1_1mm_brain.nii.gz uint8 [182, 218, 182] 1.00x1.00x1.00   [  3 182 218 182   1   1   1   1]  8
/usr/share/data/fsl-mni152-templates/MNI152lin_T1_2mm_brain.nii.gz uint8 [ 91, 109,  91] 2.00x2.00x2.00   [  3  91 109  91   1   1   1   1]  8
/usr/share/data/fsl-mni152-templates/MNI152_T1_1mm_brain.nii.gz    int16 [182, 218, 182] 1.00x1.00x1.00   [  3 182 218 182   1   1   1   1] 16
/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz    int16 [ 91, 109,  91] 2.00x2.00x2.00   [  3  91 109  91   1   1   1   1] 16
```

using '*' as argument would spit out all the header fields

Author: matthew-brett

bin/nib-ls

@@ -13,7 +13,7 @@ Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
 from __future__ import division, print_function, absolute_import
 
 __author__ = 'Yaroslav Halchenko'
-__copyright__ = 'Copyright (c) 2011-2012 Yaroslav Halchenko ' \
+__copyright__ = 'Copyright (c) 2011-2015 Yaroslav Halchenko ' \
                 'and NiBabel contributors'
 __license__ = 'MIT'
 
@@ -141,6 +141,10 @@ def get_opt_parser():
                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"),
@@ -180,6 +184,23 @@ def proc_file(f, opts):
     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 += [ 'error' ]
+
     try:
         if (hasattr(h, 'get_qform') and hasattr(h, 'get_sform')
             and (h.get_qform() != h.get_sform()).any()):

nibabel/testing/__init__.py

@@ -9,6 +9,7 @@
 ''' Utilities for testing '''
 from __future__ import division, print_function
 
+import re
 import os
 import sys
 import warnings
@@ -59,6 +60,17 @@ def assert_allclose_safely(a, b, match_nans=True):
     assert_true(np.allclose(a, b))
 
 
+def assert_re_in(regex, c, flags=0):
+    """Assert that container (list, str, etc) contains entry matching the regex
+    """
+    if not isinstance(c, (list, tuple)):
+        c = [c]
+    for e in c:
+        if re.match(regex, e, flags=flags):
+            return
+    raise AssertionError("Not a single entry matched %r in %r" % (regex, c))
+
+
 def get_fresh_mod(mod_name=__name__):
     # Get this module, with warning registry empty
     my_mod = sys.modules[mod_name]

nibabel/tests/test_scripts.py

@@ -20,12 +20,13 @@
 
 from nose.tools import (assert_true, assert_false, assert_not_equal,
                         assert_equal)
+from nose import SkipTest
 
 from numpy.testing import assert_almost_equal
 
 from .scriptrunner import ScriptRunner
 from .nibabel_data import needs_nibabel_data
-from ..testing import assert_dt_equal
+from ..testing import assert_dt_equal, assert_re_in
 from .test_parrec import (DTI_PAR_BVECS, DTI_PAR_BVALS,
                           EXAMPLE_IMAGES as PARREC_EXAMPLES)
 from .test_parrec_data import BALLS, AFF_OFF
@@ -53,16 +54,69 @@ def script_test(func):
 DATA_PATH = abspath(pjoin(dirname(__file__), 'data'))
 
 
-@script_test
-def test_nib_ls():
+def check_nib_ls_example4d(opts=[], hdrs_str=""):
     # test nib-ls script
     fname = pjoin(DATA_PATH, 'example4d.nii.gz')
     expected_re = (" (int16|[<>]i2) \[128,  96,  24,   2\] "
-                   "2.00x2.00x2.20x2000.00  #exts: 2 sform$")
-    cmd = ['nib-ls', fname]
+                   "2.00x2.00x2.20x2000.00  #exts: 2%s sform$"
+                   % hdrs_str)
+    cmd = ['nib-ls'] + opts + [fname]
     code, stdout, stderr = run_command(cmd)
     assert_equal(fname, stdout[:len(fname)])
-    assert_not_equal(re.match(expected_re, stdout[len(fname):]), None)
+    assert_re_in(expected_re, stdout[len(fname):])
+
+@script_test
+def test_nib_ls():
+    yield check_nib_ls_example4d
+    yield check_nib_ls_example4d, \
+          ['-H', 'dim,bitpix'], " \[  4 128  96  24   2   1   1   1\] 16"
+
+@script_test
+def test_nib_ls_multiple():
+    # verify that correctly lists/formats for multiple files
+    fnames = [
+        pjoin(DATA_PATH, f)
+        for f in ('example4d.nii.gz', 'example_nifti2.nii.gz',
+                  'small.mnc', 'nifti2.hdr')
+    ]
+    code, stdout, stderr = run_command(['nib-ls'] + fnames)
+    stdout_lines = stdout.split('\n')
+    assert_equal(len(stdout_lines), 4)
+    try:
+        load(pjoin(DATA_PATH, 'small.mnc'))
+    except:
+        raise SkipTest("For the other tests should be able to load MINC files")
+
+    # they should be indented correctly.  Since all files are int type -
+    ln = max(len(f) for f in fnames)
+    assert_equal([l[ln:ln+2] for l in stdout_lines], [' i']*4,
+                 msg="Type sub-string didn't start with 'i'. "
+                     "Full output was: %s" % stdout_lines)
+    # and if disregard type indicator which might vary
+    assert_equal(
+        [l[l.index('['):] for l in stdout_lines],
+        [
+            '[128,  96,  24,   2] 2.00x2.00x2.20x2000.00  #exts: 2 sform',
+            '[ 32,  20,  12,   2] 2.00x2.00x2.20x2000.00  #exts: 2 sform',
+            '[ 18,  28,  29]      9.00x8.00x7.00',
+            '[ 91, 109,  91]      2.00x2.00x2.00'
+        ]
+    )
+
+    # Now run with -s for stats
+    code, stdout, stderr = run_command(['nib-ls', '-s'] + fnames)
+    stdout_lines = stdout.split('\n')
+    assert_equal(len(stdout_lines), 4)
+    assert_equal(
+        [l[l.index('['):] for l in stdout_lines],
+        [
+            '[128,  96,  24,   2] 2.00x2.00x2.20x2000.00  #exts: 2 sform [229725]   2:1.2e+03',
+            '[ 32,  20,  12,   2] 2.00x2.00x2.20x2000.00  #exts: 2 sform  [15360]  46:7.6e+02',
+            '[ 18,  28,  29]      9.00x8.00x7.00                          [14616]    0.12:93',
+            '[ 91, 109,  91]      2.00x2.00x2.00                           error'
+        ]
+    )
+
 
 
 @script_test

nibabel/tests/test_testing.py

@@ -11,7 +11,7 @@
 from nose.tools import assert_raises
 from ..testing import (error_warnings, suppress_warnings,
                        clear_and_catch_warnings, assert_allclose_safely,
-                       get_fresh_mod)
+                       get_fresh_mod, assert_re_in)
 
 
 def assert_warn_len_equal(mod, n_in_context):
@@ -145,3 +145,24 @@ def f():
         with suppress_warnings():
             raise ValueError('An error')
     assert_raises(ValueError, f)
+
+
+def test_assert_re_in():
+    assert_re_in(".*", "")
+    assert_re_in(".*", ["any"])
+
+    # Should do match not search
+    assert_re_in("ab", "abc")
+    assert_raises(AssertionError, assert_re_in, "ab", "cab")
+    assert_raises(AssertionError, assert_re_in, "ab$", "abc")
+
+    # Sufficient to have one entry matching
+    assert_re_in("ab", ["", "abc", "laskdjf"])
+    assert_raises(AssertionError, assert_re_in, "ab$", ["ddd", ""])
+
+    # Tuples should be ok too
+    assert_re_in("ab", ("", "abc", "laskdjf"))
+    assert_raises(AssertionError, assert_re_in, "ab$", ("ddd", ""))
+
+    # Shouldn't "match" the empty list
+    assert_raises(AssertionError, assert_re_in, "", [])