ENH+RF: nib-ls -c/--counts to report counts for each value (useful for ROI maps)

Also adjusted slightly output of --stats to include range in [from, to]

Author: yarikoptic

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) 2011-2015 Yaroslav Halchenko ' \
+__copyright__ = 'Copyright (c) 2011-2016 Yaroslav Halchenko ' \
                 'and NiBabel contributors'
 __license__ = 'MIT'
 
@@ -22,6 +22,7 @@ import sys
 from math import ceil
 from optparse import OptionParser, Option
 from io import StringIO
+from collections import Counter
 
 import numpy as np
 
@@ -149,6 +150,10 @@ def get_opt_parser():
                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("-z", "--zeros",
                action="store_true", dest='stats_zeros', default=False,
                help="Include zeros into output basic data statistics (--stats)"),
@@ -214,18 +219,24 @@ def proc_file(f, opts):
         else:
             row += ['error']
 
-    if opts.stats:
+    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)]
-            # just # of elements
-            row += ["[%d] " % np.prod(d.shape)]
-            # stats
-            row += [len(d) and '%.2g:%.2g' % (np.min(d), np.max(d)) or '-']
+            if opts.stats:
+                # just # of elements
+                row += ["[%d]" % np.prod(d.shape)]
+                # stats
+                row += [len(d) and '[%.2g, %.2g]' % (np.min(d), np.max(d)) or '-']
+            if opts.counts:
+                counter = Counter()
+                counter.update(d.flatten())
+                # go through each entry and report only non-0 ones
+                row += [" ".join("%g:%d" % (i, counter[i]) for i in sorted(counter))]
         except Exception as e:
-            verbose(2, "Failed to obtain stats -- %s" % str(e))
+            verbose(2, "Failed to obtain stats/counts -- %s" % str(e))
             row += ['error']
     return row
 

nibabel/tests/test_scripts.py

@@ -53,12 +53,12 @@ def script_test(func):
 DATA_PATH = abspath(pjoin(dirname(__file__), 'data'))
 
 
-def check_nib_ls_example4d(opts=[], hdrs_str=""):
+def check_nib_ls_example4d(opts=[], hdrs_str="", other_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%s sform$"
-                   % hdrs_str)
+                   "2.00x2.00x2.20x2000.00  #exts: 2%s sform%s$"
+                   % (hdrs_str, other_str))
     cmd = ['nib-ls'] + opts + [fname]
     code, stdout, stderr = run_command(cmd)
     assert_equal(fname, stdout[:len(fname)])
@@ -68,7 +68,15 @@ def check_nib_ls_example4d(opts=[], hdrs_str=""):
 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"
+        ['-H', 'dim,bitpix'], " \[  4 128  96  24   2   1   1   1\] 16"
+    yield check_nib_ls_example4d, ['-c'], "", " 2:3 3:2 4:1 5:1.*"
+    # both stats and counts
+    yield check_nib_ls_example4d, \
+        ['-c', '-s'], "", " \[229725\] \[2, 1.2e\+03\] 2:3 3:2 4:1 5:1.*"
+    # and must not error out if we allow for zeros
+    yield check_nib_ls_example4d, \
+        ['-c', '-s', '-z'], "", " \[589824\] \[0, 1.2e\+03\] 0:360099 2:3 3:2 4:1 5:1.*"
+
 
 @script_test
 def test_nib_ls_multiple():